Increased Chain Length Promotes Pneumococcal Adherence and Colonization

PubMed Central

Rodriguez, Jesse L.; Dalia, Ankur B.

2012-01-01

Streptococcus pneumoniae is a mucosal pathogen that grows in chains of variable lengths. Short-chain forms are less likely to activate complement, and as a consequence they evade opsonophagocytic clearance more effectively during invasive disease. When grown in human nasal airway surface fluid, pneumococci exhibited both short- and long-chain forms. Here, we determined whether longer chains provide an advantage during colonization when the organism is attached to the epithelial surface. Chain-forming mutants and the parental strain grown under conditions to promote chain formation showed increased adherence to human epithelial cells (A549 cells) in vitro. Additionally, adherence to A549 cells selected for longer chains within the wild-type strain. In vivo in a murine model of colonization, chain-forming mutants outcompeted the parental strain. Together, our results demonstrate that morphological heterogeneity in the pneumococcus may promote colonization of the upper respiratory tract by enhancing the ability of the organism to bind to the epithelial surface. PMID:22825449

Perceptual and Neural Olfactory Similarity in Honeybees

PubMed Central

Sandoz, Jean-Christophe

2005-01-01

The question of whether or not neural activity patterns recorded in the olfactory centres of the brain correspond to olfactory perceptual measures remains unanswered. To address this question, we studied olfaction in honeybees Apis mellifera using the olfactory conditioning of the proboscis extension response. We conditioned bees to odours and tested generalisation responses to different odours. Sixteen odours were used, which varied both in their functional group (primary and secondary alcohols, aldehydes and ketones) and in their carbon-chain length (from six to nine carbons).The results obtained by presentation of a total of 16 × 16 odour pairs show that (i) all odorants presented could be learned, although acquisition was lower for short-chain ketones; (ii) generalisation varied depending both on the functional group and the carbon-chain length of odours trained; higher generalisation was found between long-chain than between short-chain molecules and between groups such as primary and secondary alcohols; (iii) for some odour pairs, cross-generalisation between odorants was asymmetric; (iv) a putative olfactory space could be defined for the honeybee with functional group and carbon-chain length as inner dimensions; (v) perceptual distances in such a space correlate well with physiological distances determined from optophysiological recordings of antennal lobe activity. We conclude that functional group and carbon-chain length are inner dimensions of the honeybee olfactory space and that neural activity in the antennal lobe reflects the perceptual quality of odours. PMID:15736975

Anti-proliferative effects of O-acyl-low-molecular-weight heparin derivatives on bovine pulmonary artery smooth muscle cells.

PubMed

Garg, Hari G; Mrabat, Hicham; Yu, Lunyin; Hales, Charles A; Li, Boyangzi; Moore, Casey N; Zhang, Fuming; Linhardt, Robert J

2011-08-01

Heparin (HP) inhibits the growth of several cell types in vitro including bovine pulmonary artery (BPA) smooth muscle cells (SMCs). In initial studies we discovered that an O-hexanoylated low-molecular-weight (LMW) HP derivative having acyl groups with 6-carbon chain length was more potent inhibitor of BPA-SMCs than the starting HP. We prepared several O-acylated LMWHP derivatives having 4-, 6-, 8-, 10-, 12-, and 18- carbon acyl chain lengths to determine the optimal acyl chain length for maximum anti-proliferative properties of BPA-SMCs. The starting LMWHP was prepared from unfractionated HP by sodium periodate treatment followed by sodium borohydride reduction. The tri-n-butylammonium salt of this LMWHP was O-acylated with butanoic, hexanoic, octanoic, decanoic, dodecanoic, and stearyl anhydrides separately to give respective O-acylated LMWHP derivatives. Gradient polyacrylamide gel electrophoresis (PAGE) was used to examine the average molecular weights of those O-acylated LMWHP derivatives. NMR analysis indicated the presence of one O-acyl group per disaccharide residue. Measurement of the inhibition of BPA-SMCS as a function of O-acyl chain length shows two optima, at a carbon chain length of 6 (O-hexanoylated LMWHP) and at a carbon chain length 12-18 (O-dodecanoyl and O-stearyl LMWHPs). A solution competition SPR study was performed to test the ability of different O-acylated LMWHP derivatives to inhibit fibroblast growth factor (FGF) 1 and FGF2 binding to surface-immobilized heparin. All the LMWHP derivatives bound to FGF1 and FGF2 but each exhibited slightly different binding affinity.

The Twilight Zone between Protein Order and Disorder

PubMed Central

Szilágyi, A.; Györffy, D.; Závodszky, P.

2008-01-01

The amino acid composition of intrinsically disordered proteins and protein segments characteristically differs from that of ordered proteins. This observation forms the basis of several disorder prediction methods. These, however, usually perform worse for smaller proteins (or segments) than for larger ones. We show that the regions of amino acid composition space corresponding to ordered and disordered proteins overlap with each other, and the extent of the overlap (the “twilight zone”) is larger for short than for long chains. To explain this finding, we used two-dimensional lattice model proteins containing hydrophobic, polar, and charged monomers and revealed the relation among chain length, amino acid composition, and disorder. Because the number of chain configurations exponentially grows with chain length, a larger fraction of longer chains can reach a low-energy, ordered state than do shorter chains. The amount of information carried by the amino acid composition about whether a protein or segment is (dis)ordered grows with increasing chain length. Smaller proteins rely more on specific interactions for stability, which limits the possible accuracy of disorder prediction methods. For proteins in the “twilight zone”, size can determine order, as illustrated by the example of two-state homodimers. PMID:18441033

The twilight zone between protein order and disorder.

PubMed

Szilágyi, A; Györffy, D; Závodszky, P

2008-08-01

The amino acid composition of intrinsically disordered proteins and protein segments characteristically differs from that of ordered proteins. This observation forms the basis of several disorder prediction methods. These, however, usually perform worse for smaller proteins (or segments) than for larger ones. We show that the regions of amino acid composition space corresponding to ordered and disordered proteins overlap with each other, and the extent of the overlap (the "twilight zone") is larger for short than for long chains. To explain this finding, we used two-dimensional lattice model proteins containing hydrophobic, polar, and charged monomers and revealed the relation among chain length, amino acid composition, and disorder. Because the number of chain configurations exponentially grows with chain length, a larger fraction of longer chains can reach a low-energy, ordered state than do shorter chains. The amount of information carried by the amino acid composition about whether a protein or segment is (dis)ordered grows with increasing chain length. Smaller proteins rely more on specific interactions for stability, which limits the possible accuracy of disorder prediction methods. For proteins in the "twilight zone", size can determine order, as illustrated by the example of two-state homodimers.

A kinetic theory description of the viscosity of dense fluids consisting of chain molecules.

PubMed

de Wijn, Astrid S; Vesovic, Velisa; Jackson, George; Trusler, J P Martin

2008-05-28

An expression for the viscosity of a dense fluid is presented that includes the effect of molecular shape. The molecules of the fluid are approximated by chains of equal-sized, tangentially jointed, rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions between two rigid spheres belonging to different chains. The approach is thus analogous to that of Enskog for a fluid consisting of rigid spheres. The description is developed in terms of two molecular parameters, the diameter sigma of the spherical segment and the chain length (number of segments) m. It is demonstrated that an analysis of viscosity data of a particular pure fluid alone cannot be used to obtain independently effective values of both sigma and m. Nevertheless, the chain lengths of n-alkanes are determined by assuming that the diameter of each rigid sphere making up the chain can be represented by the diameter of a methane molecule. The effective chain lengths of n-alkanes are found to increase linearly with the number C of carbon atoms present. The dependence can be approximated by a simple relationship m=1+(C-1)3. The same relationship was reported within the context of a statistical associating fluid theory equation of state treatment of the fluid, indicating that both the equilibrium thermodynamic properties and viscosity yield the same value for the chain lengths of n-alkanes.

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

PubMed

Kuo, Hsiou-Ting; Liu, Shing-Lung; Chiu, Wen-Chieh; Fang, Chun-Jen; Chang, Hsien-Chen; Wang, Wei-Ren; Yang, Po-An; Li, Jhe-Hao; Huang, Shing-Jong; Huang, Shou-Ling; Cheng, Richard P

2015-05-01

β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.

Stability of vertical magnetic chains

PubMed Central

2017-01-01

A linear stability analysis is performed for a pair of coaxial vertical chains made from permanently magnetized balls under the influence of gravity. While one chain rises from the ground, the other hangs from above, with the remaining ends separated by a gap of prescribed length. Various boundary conditions are considered, as are situations in which the magnetic dipole moments in the two chains are parallel or antiparallel. The case of a single chain attached to the ground is also discussed. The stability of the system is examined with respect to three quantities: the number of balls in each chain, the length of the gap between the chains, and a single dimensionless parameter which embodies the competition between magnetic and gravitational forces. Asymptotic scaling laws involving these parameters are provided. The Hessian matrix is computed in exact form, allowing the critical parameter values at which the system loses stability and the respective eigenmodes to be determined up to machine precision. A comparison with simple experiments for a single chain attached to the ground shows good agreement. PMID:28293135

Stability of vertical magnetic chains

NASA Astrophysics Data System (ADS)

Schönke, Johannes; Fried, Eliot

2017-02-01

A linear stability analysis is performed for a pair of coaxial vertical chains made from permanently magnetized balls under the influence of gravity. While one chain rises from the ground, the other hangs from above, with the remaining ends separated by a gap of prescribed length. Various boundary conditions are considered, as are situations in which the magnetic dipole moments in the two chains are parallel or antiparallel. The case of a single chain attached to the ground is also discussed. The stability of the system is examined with respect to three quantities: the number of balls in each chain, the length of the gap between the chains, and a single dimensionless parameter which embodies the competition between magnetic and gravitational forces. Asymptotic scaling laws involving these parameters are provided. The Hessian matrix is computed in exact form, allowing the critical parameter values at which the system loses stability and the respective eigenmodes to be determined up to machine precision. A comparison with simple experiments for a single chain attached to the ground shows good agreement.

Kinetics of interior loop formation in semiflexible chains.

PubMed

Hyeon, Changbong; Thirumalai, D

2006-03-14

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.

Multiple scales and phases in discrete chains with application to folded proteins

NASA Astrophysics Data System (ADS)

Sinelnikova, A.; Niemi, A. J.; Nilsson, Johan; Ulybyshev, M.

2018-05-01

Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein. Here we address this impending problem. We develop a methodology with the potential to systematically identify different length scales, in the general case of a linear polymer chain. For this we introduce and analyze the properties of an order parameter that can both reveal the presence of different length scales and can also probe the phase structure. We first develop our concepts in the case of chiral homopolymers. We introduce a variant of Kadanoff's block-spin transformation to coarse grain piecewise linear chains, such as the C α backbone of a protein. We derive analytically, and then verify numerically, a number of properties that the order parameter can display, in the case of a chiral polymer chain. In particular, we propose that in the case of a chiral heteropolymer the order parameter can reveal traits of several different phases, contingent on the length scale at which it is scrutinized. We confirm that this is the case with crystallographic protein structures in the Protein Data Bank. Thus our results suggest relations between the scales, the phases, and the complexity of folding pathways.

Characterization of Site-Specific Mutations in a Short-Chain-Length/Medium-Chain-Length Polyhydroxyalkanoate Synthase: In Vivo and In Vitro Studies of Enzymatic Activity and Substrate Specificity

PubMed Central

Chuah, Jo-Ann; Tomizawa, Satoshi; Yamada, Miwa; Tsuge, Takeharu; Doi, Yoshiharu

2013-01-01

Saturation point mutagenesis was carried out at position 479 in the polyhydroxyalkanoate (PHA) synthase from Chromobacterium sp. strain USM2 (PhaCCs) with specificities for short-chain-length (SCL) [(R)-3-hydroxybutyrate (3HB) and (R)-3-hydroxyvalerate (3HV)] and medium-chain-length (MCL) [(R)-3-hydroxyhexanoate (3HHx)] monomers in an effort to enhance the specificity of the enzyme for 3HHx. A maximum 4-fold increase in 3HHx incorporation and a 1.6-fold increase in PHA biosynthesis, more than the wild-type synthase, was achieved using selected mutant synthases. These increases were subsequently correlated with improved synthase activity and increased preference of PhaCCs for 3HHx monomers. We found that substitutions with uncharged residues were beneficial, as they resulted in enhanced PHA production and/or 3HHx incorporation. Further analysis led to postulations that the size and geometry of the substrate-binding pocket are determinants of PHA accumulation, 3HHx fraction, and chain length specificity. In vitro activities for polymerization of 3HV and 3HHx monomers were consistent with in vivo substrate specificities. Ultimately, the preference shown by wild-type and mutant synthases for either SCL (C4 and C5) or MCL (C6) substrates substantiates the fundamental classification of PHA synthases. PMID:23584780

Thermodynamics of Inozemtsev's elliptic spin chain

NASA Astrophysics Data System (ADS)

Klabbers, Rob

2016-06-01

We study the thermodynamic behaviour of Inozemtsev's long-range elliptic spin chain using the Bethe ansatz equations describing the spectrum of the model in the infinite-length limit. We classify all solutions of these equations in that limit and argue which of these solutions determine the spectrum in the thermodynamic limit. Interestingly, some of the solutions are not selfconjugate, which puts the model in sharp contrast to one of the model's limiting cases, the Heisenberg XXX spin chain. Invoking the string hypothesis we derive the thermodynamic Bethe ansatz equations (TBA-equations) from which we determine the Helmholtz free energy in thermodynamic equilibrium and derive the associated Y-system. We corroborate our results by comparing numerical solutions of the TBA-equations to a direct computation of the free energy for the finite-length hamiltonian. In addition we confirm numerically the interesting conjecture put forward by Finkel and González-López that the original and supersymmetric versions of Inozemtsev's elliptic spin chain are equivalent in the thermodynamic limit.

Configurations and Dynamics of Semi-Flexible Polymers in Good and Poor Solvents

NASA Astrophysics Data System (ADS)

Larson, Ronald

We develop coarse-graining procedures for determining the conformational and dynamic behavior of semi-flexible chains with and without flow using Brownian dynamics (BD) simulations that are insensitive to the degree of coarse-graining. In the absence of flow, in a poor solvent, we find three main collapsed states: torus, bundle, and globule over a range of dimensionless ratios of the three energy parameters, namely solvent-polymer surface energy, energy of polymer folds, and polymer bending energy or persistence length. A theoretical phase diagram, confirmed by BD simulations, captures the general phase behavior of a single long chain (>10 Kuhn lengths) at moderately high (order unity) dimensionless temperature, which is the ratio of thermal energy to the attractive interaction between neighboring monomers. We also find converged results for polymer conformations in shear or extensional flow in solvents of various qualities and determine scaling laws for chain dimensions for low, moderate, and high Weissenberg numbers Wi. We also derive scaling laws to describe chains dimensions and tumbling rates in these regimes.

Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

DOE PAGES

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; ...

2017-06-01

We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

Vapor-liquid equilibrium and critical asymmetry of square well and short square well chain fluids.

PubMed

Li, Liyan; Sun, Fangfang; Chen, Zhitong; Wang, Long; Cai, Jun

2014-08-07

The critical behavior of square well fluids with variable interaction ranges and of short square well chain fluids have been investigated by grand canonical ensemble Monte Carlo simulations. The critical temperatures and densities were estimated by a finite-size scaling analysis with the help of histogram reweighting technique. The vapor-liquid coexistence curve in the near-critical region was determined using hyper-parallel tempering Monte Carlo simulations. The simulation results for coexistence diameters show that the contribution of |t|(1-α) to the coexistence diameter dominates the singular behavior in all systems investigated. The contribution of |t|(2β) to the coexistence diameter is larger for the system with a smaller interaction range λ. While for short square well chain fluids, longer the chain length, larger the contribution of |t|(2β). The molecular configuration greatly influences the critical asymmetry: a short soft chain fluid shows weaker critical asymmetry than a stiff chain fluid with same chain length.

Ballistic heat conduction and mass disorder in one dimension.

PubMed

Ong, Zhun-Yong; Zhang, Gang

2014-08-20

It is well-known that in the disordered harmonic chain, heat conduction is subballistic and the thermal conductivity (κ) scales asymptotically as lim(L--> ∞) κ ∝ L(0.5) where L is the chain length. However, using the nonequilibrium Green's function (NEGF) method and analytical modelling, we show that there exists a critical crossover length scale (LC) below which ballistic heat conduction (κ ∝ L) can coexist with mass disorder. This ballistic-to-subballistic heat conduction crossover is connected to the exponential attenuation of the phonon transmittance function Ξ i.e. Ξ(ω, L) = exp[-L/λ(ω)], where λ is the frequency-dependent attenuation length. The crossover length can be determined from the minimum attenuation length, which depends on the maximum transmitted frequency. We numerically determine the dependence of the transmittance on frequency and mass composition as well as derive a closed form estimate, which agrees closely with the numerical results. For the length-dependent thermal conductance, we also derive a closed form expression which agrees closely with numerical results and reproduces the ballistic to subballistic thermal conduction crossover. This allows us to characterize the crossover in terms of changes in the length, mass composition and temperature dependence, and also to determine the conditions under which heat conduction enters the ballistic regime. We describe how the mass composition can be modified to increase ballistic heat conduction.

Transport of triplet excitons along continuous 100 nm polyfluorene chains

DOE PAGES

Xi, Liang; Bird, Matthew; Mauro, Gina; ...

2014-12-03

Triplet excitons created in poly-2,7-(9,9-dihexyl)fluorene (pF) chains with end trap groups in solution are efficiently transported to and captured by the end groups. The triplets explore the entire lengths of the chains, even for ~100 nm long chains enabling determination of the completeness of end capping. The results show that the chains continuous: they may contain transient barriers or traps, such as those from fluctuations of dihedral angles, but are free of major defects that stop motion of the triplets. Quantitative determinations are aided by the addition of a strong electron donor, TMPD, which removes absorption bands of the end-trappedmore » triplets. For chains having at least one end trap, triplet capture is quantitative on the 1 µs timescale imposed by the use of the donor. Fractions of chains having no end traps were 0.15 for pF samples with anthraquinone (AQ) end traps and 0.063 with naphthylimide (NI) end traps. These determinations agreed with measurements by NMR for short (<40 polymer repeat units (PRU)) chains, where NMR determinations are accurate. The results find no evidence for traps or barriers to transport of triplets, and places limits on the possible presence of defects as impenetrable barriers to less than one per 300 PRU. The present results present a paradigm different from the current consensus, derived from observations of singlet excitons, that conjugated chains are divided into “segments,” perhaps by some kind of defects. For the present pF chains, the segmentation either does not apply to triplet excitons or is transient so that the defects are healed or surmounted in times much shorter than 1 µs. Triplets on chains without end trap groups transfer to chains with end traps on a slower time scale. Rate constants for these bimolecular triplet transfer reactions were found to increase with the length of the accepting chain, as did rate constants for triplet transfer to the chains from small molecules like biphenyl. As a result, a second set of polyfluorenes with 2-butyloctyl side chains was found to have a much lower completeness of end capping.« less

Swelling of biological and semiflexible polyelectrolytes.

PubMed

Dobrynin, Andrey V; Carrillo, Jan-Michael Y

2009-10-21

We have developed a theoretical model of swelling of semiflexible (biological) polyelectrolytes in salt solutions. Our approach is based on separation of length scales which allowed us to split a chain's electrostatic energy into two parts that describe local and remote electrostatic interactions along the polymer backbone. The local part takes into account interactions between charged monomers that are separated by distances along the polymer backbone shorter than the chain's persistence length. These electrostatic interactions renormalize chain persistence length. The second part includes electrostatic interactions between remote charged pairs along the polymer backbone located at distances larger than the chain persistence length. These interactions are responsible for chain swelling. In the framework of this approach we calculated effective chain persistence length and chain size as a function of the Debye screening length, chain degree of ionization, bare persistence length and chain degree of polymerization. Our crossover expression for the effective chain's persistence length is in good quantitative agreement with the experimental data on DNA. We have been able to fit experimental datasets by using two adjustable parameters: DNA ionization degree (α = 0.15-0.17) and a bare persistence length (l(p) = 40-44 nm).

Ultrasonic Relaxation Study of 1-Alkyl-3-methylimidazolium-Based Room-Temperature Ionic Liquids: Probing the Role of Alkyl Chain Length in the Cation.

PubMed

Zorębski, Michał; Zorębski, Edward; Dzida, Marzena; Skowronek, Justyna; Jężak, Sylwia; Goodrich, Peter; Jacquemin, Johan

2016-04-14

Ultrasound absorption spectra of four 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imides were determined as a function of the alkyl chain length on the cation from 1-propyl to 1-hexyl from 293.15 to 323.15 K at ambient pressure. Herein, the ultrasound absorption measurements were carried out using a standard pulse technique within a frequency range from 10 to 300 MHz. Additionally, the speed of sound, density, and viscosity have been measured. The presence of strong dissipative processes during the ultrasound wave propagation was found experimentally, i.e., relaxation processes in the megahertz range were observed for all compounds over the whole temperature range. The relaxation spectra (both relaxation amplitude and relaxation frequency) were shown to be dependent on the alkyl side chain length of the 1-alkyl-3-methylimidazolium ring. In most cases, a single-Debye model described the absorption spectra very well. However, a comparison of the determined spectra with the spectra of a few other imidazolium-based ionic liquids reported in the literature (in part recalculated in this work) shows that the complexity of the spectra increases rapidly with the elongation of the alkyl chain length on the cation. This complexity indicates that both the volume viscosity and the shear viscosity are involved in relaxation processes even in relatively low frequency ranges. As a consequence, the sound velocity dispersion is present at relatively low megahertz frequencies.

Weak polyelectrolyte complexation driven by associative charging.

PubMed

Rathee, Vikramjit S; Zervoudakis, Aristotle J; Sidky, Hythem; Sikora, Benjamin J; Whitmer, Jonathan K

2018-03-21

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Weak polyelectrolyte complexation driven by associative charging

NASA Astrophysics Data System (ADS)

Rathee, Vikramjit S.; Zervoudakis, Aristotle J.; Sidky, Hythem; Sikora, Benjamin J.; Whitmer, Jonathan K.

2018-03-01

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

The snakelike chain character of unstructured RNA.

PubMed

Jacobson, David R; McIntosh, Dustin B; Saleh, Omar A

2013-12-03

In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod "wormlike chain" (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a "snakelike chain," characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Xi, Liang; Bird, Matthew; Mauro, Gina

Triplet excitons created in poly-2,7-(9,9-dihexyl)fluorene (pF) chains with end trap groups in solution are efficiently transported to and captured by the end groups. The triplets explore the entire lengths of the chains, even for ~100 nm long chains enabling determination of the completeness of end capping. The results show that the chains continuous: they may contain transient barriers or traps, such as those from fluctuations of dihedral angles, but are free of major defects that stop motion of the triplets. Quantitative determinations are aided by the addition of a strong electron donor, TMPD, which removes absorption bands of the end-trappedmore » triplets. For chains having at least one end trap, triplet capture is quantitative on the 1 µs timescale imposed by the use of the donor. Fractions of chains having no end traps were 0.15 for pF samples with anthraquinone (AQ) end traps and 0.063 with naphthylimide (NI) end traps. These determinations agreed with measurements by NMR for short (<40 polymer repeat units (PRU)) chains, where NMR determinations are accurate. The results find no evidence for traps or barriers to transport of triplets, and places limits on the possible presence of defects as impenetrable barriers to less than one per 300 PRU. The present results present a paradigm different from the current consensus, derived from observations of singlet excitons, that conjugated chains are divided into “segments,” perhaps by some kind of defects. For the present pF chains, the segmentation either does not apply to triplet excitons or is transient so that the defects are healed or surmounted in times much shorter than 1 µs. Triplets on chains without end trap groups transfer to chains with end traps on a slower time scale. Rate constants for these bimolecular triplet transfer reactions were found to increase with the length of the accepting chain, as did rate constants for triplet transfer to the chains from small molecules like biphenyl. As a result, a second set of polyfluorenes with 2-butyloctyl side chains was found to have a much lower completeness of end capping.« less

Structure-Antibacterial Activity Relationships of Imidazolium-Type Ionic Liquid Monomers, Poly(ionic liquids) and Poly(ionic liquid) Membranes: Effect of Alkyl Chain Length and Cations.

PubMed

Zheng, Zhiqiang; Xu, Qiming; Guo, Jiangna; Qin, Jing; Mao, Hailei; Wang, Bin; Yan, Feng

2016-05-25

The structure-antibacterial activity relationship between the small molecular compounds and polymers are still elusive. Here, imidazolium-type ionic liquid (IL) monomers and their corresponding poly(ionic liquids) (PILs) and poly(ionic liquid) membranes were synthesized. The effect of chemical structure, including carbon chain length of substitution at the N3 position and charge density of cations (mono- or bis-imidazolium) on the antimicrobial activities against both Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was investigated by determination of minimum inhibitory concentration (MIC). The antibacterial activities of both ILs and PILs were improved with the increase of the alkyl chain length and higher charge density (bis-cations) of imidazolium cations. Moreover, PILs exhibited lower MIC values relative to the IL monomers. However, the antibacterial activities of PIL membranes showed no correlation to those of their analogous small molecule IL monomers and PILs, which increased with the charge density (bis-cations) while decreasing with the increase of alkyl chain length. The results indicated that antibacterial property studies on small molecules and homopolymers may not provide a solid basis for evaluating that in corresponding polymer membranes.

Relationship between peroxisome proliferator-activated receptor alpha activity and cellular concentration of 14 perfluoroalkyl substances in HepG2 cells.

PubMed

Rosenmai, Anna Kjerstine; Ahrens, Lutz; le Godec, Théo; Lundqvist, Johan; Oskarsson, Agneta

2018-02-01

Peroxisome proliferator-activated receptor alpha (PPARα) is a molecular target for perfluoroalkyl substances (PFASs). Little is known about the cellular uptake of PFASs and how it affects the PPARα activity. We investigated the relationship between PPARα activity and cellular concentration in HepG2 cells of 14 PFASs, including perfluoroalkyl carboxylates (PFCAs), perfluoroalkyl sulfonates and perfluorooctane sulfonamide (FOSA). Cellular concentrations were determined by high-performance liquid chromatography-tandem mass spectrometry and PPARα activity was determined in transiently transfected cells by reporter gene assay. Cellular uptake of the PFASs was low (0.04-4.1%) with absolute cellular concentrations in the range 4-2500 ng mg -1 protein. Cellular concentration of PFCAs increased with perfluorocarbon chain length up to perfluorododecanoate. PPARα activity of PFCAs increased with chain length up to perfluorooctanoate. The maximum induction of PPARα activity was similar for short-chain (perfluorobutanoate and perfluoropentanoate) and long-chain PFCAs (perfluorododecanoate and perfluorotetradecanoate) (approximately twofold). However, PPARα activities were induced at lower cellular concentrations for the short-chain homologs compared to the long-chain homologs. Perfluorohexanoate, perfluoroheptanoate, perfluorooctanoate, perfluorononanoate (PFNA) and perfluorodecanoate induced PPARα activities >2.5-fold compared to controls. The concentration-response relationships were positive for all the tested compounds, except perfluorooctane sulfonate PFOS and FOSA, and were compound-specific, as demonstrated by differences in the estimated slopes. The relationships were steeper for PFCAs with chain lengths up to and including PFNA than for the other studied PFASs. To our knowledge, this is the first report establishing relationships between PPARα activity and cellular concentration of a broad range of PFASs. Copyright © 2017 John Wiley & Sons, Ltd.

The Study of Interpenetration Length between dPS Films and PS-grafted Layers

NASA Astrophysics Data System (ADS)

Lee, Hoyeon; Jo, Seongjun; Hirata, Toyoaki; Yamada, Norifumi L.; Tanaka, Keiji; Ryu, Du Yeol

In polymer thin film system, the type of interfacial interaction is a critical parameter to determining the thermal and physical properties of polymer films. Interestingly, the interfacial energy of grafted substrates with polymer chains is remarkably altered by simply controlling grafting density, which has been referred to as autophobicity. In this study, we investigated the interpenetrating interfaces between deuterated polystyrene (dPS) and grafted substrates with the same chemical identity. PS-grafted substrates were prepared using a grafting-to approach with hydroxyl end-functionalized polystyrene (PSOH) in a dry brush regime, where the brush thickness and grafting density were determined based on the chain length (or molecular weight, Mn) of PSOHs. The interpenetration lengths (ξ) at interfaces between dPS and PS-grafted layers were characterized using neutron reflectivity (NR) measurements (performed at the SOFIA beam-line at J-PARC, Japan). Academic adviser.

Biophysical Interactions Control the Size and Abundance of Large Phytoplankton Chains at the Ushant Tidal Front

PubMed Central

Landeira, José M.; Ferron, Bruno; Lunven, Michel; Morin, Pascal; Marié, Louis; Sourisseau, Marc

2014-01-01

Phytoplankton blooms are usually dominated by chain-forming diatom species that can alter food pathways from primary producers to predators by reducing the interactions between intermediate trophic levels. The food-web modifications are determined by the length of the chains; however, the estimation is biased because traditional sampling strategies damage the chains and, therefore, change the phytoplankton size structure. Sedimentological studies around oceanic fronts have shown high concentrations of giant diatom mats (>1 cm in length), suggesting that the size of diatom chains is underestimated in the pelagic realm. Here, we investigate the variability in size and abundance of phytoplankton chains at the Ushant tidal front (NW France) using the Video Fluorescence Analyzer (VFA), a novel and non-invasive system. CTD and Scanfish profiling characterized a strong temperature and chlorophyll front, separating mixed coastal waters from the oceanic-stratified domain. In order to elucidate spring-neap variations in the front, vertical microstructure profiler was used to estimate the turbulence and vertical nitrate flux. Key findings were: (1) the VFA system recorded large diatom chains up to 10.7 mm in length; (2) chains were mainly distributed in the frontal region, with maximum values above the pycnocline in coincidence with the maximum chlorophyll; (3) the diapycnal fluxes of nitrate enabled the maintenance of the bloom in the frontal area throughout the spring-neap tidal cycle; (4) from spring to neap tide the chains length was significantly reduced; (5) during neap tide, the less intense vertical diffusion of nutrients, as well as the lower turbulence around the chains, intensified nutrient-depleted conditions and, thus, very large chains became disadvantageous. To explain this pattern, we suggest that size plasticity is an important ecological trait driving phytoplankton species competition. Although this plasticity behavior is well known from experiments in the laboratory, it has never been reported from observations in the field. PMID:24587384

Lipophilization of somatostatin analog RC-160 improves its bioactivity and stability.

PubMed

Dasgupta, P; Singh, A T; Mukherjee, R

1999-07-01

Acromegaly is a symptomatically disabling condition, resulting from a growth hormone (GH) secreting pituitary tumor. The somatostatin analog RC- 160 is known to potently inhibit hypersecretion of GH, from pituitary adenomas. However, the therapeutic potential of RC-160, is limited by its short serum half life. To overcome this limitation, fatty acids with carbon chain lengths ranging from 4 to 18 were conjugated to RC-160. The GH-inhibitory activity of these lipopeptides, as well as their binding profile to somatostatin receptors, on the rat pituitary adenoma cell line GH3 was studied in vitro. The relative stability of lipophilized RC-160 towards degradation by crude papaya protease was also determined. The long chain lipopeptides, like myristoyl-RC-160 (carbon chain length = 14) were found to exhibit greater receptor affinity and GH-inhibitory activity, as compared to their counterparts of lower chain lengths. However, the receptor affinity and GH-inhibitory activity of stearoyl-RC-160 (carbon chain length = 18), was found to lower than RC-160 and its lipophilized derivatives. Unlike RC-160, the myristoylated derivative was found to have significantly greater resistance to protease and serum degradation (p < 0.01). Lipophilization of RC-160 with long chain fatty acids improves its stability and GH-inhibitory activity. The activity of lipophilized RC-160 seems to increase with increasing hydrophobicity of the lipopeptide, and reaches a maxima at myristoyl-RC-160 for GH3. Hence, optimizing the hydrophobicity should be an important consideration governing the design and synthesis of bioactive lipopeptides.

Supramolecular Polymers Based on Non-Coplanar AAA-DDD Hydrogen-Bonded Complexes.

PubMed

Mendez, Iamnica J Linares; Wang, Hong-Bo; Yuan, Ying-Xue; Wisner, James A

2018-03-01

Non-coplanar triple-hydrogen-bond arrays are connected as telechelic groups to alkyl chains and their properties as AA/BB type supramolecular polymers are examined. Viscosity studies at three temperatures are used to study the ring-chain equilibrium and determine the critical concentrations where polymer chains are formed. It is observed that neither the temperature range studied nor the alkyl chain length of one component significantly affect the polymerization properties in this system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measurement of chain tilt angle in fully hydrated bilayers of gel phase lecithins.

PubMed Central

Tristram-Nagle, S; Zhang, R; Suter, R M; Worthington, C R; Sun, W J; Nagle, J F

1993-01-01

The tilt angle theta tilt of the hydrocarbon chains has been determined for fully hydrated gel phase of a series of saturated lecithins. Oriented samples were prepared on glass substrates and hydrated with supersaturated water vapor. Evidence for full hydration was the same intensity pattern of the low angle lamellar peaks and the same lamellar repeat D as unoriented multilamellar vesicles. Tilting the sample permitted observation of all the wide angle arcs necessary to verify the theoretical diffraction pattern corresponding to tilting of the chains towards nearest neighbors. The length of the scattering unit corresponds to two hydrocarbon chains, requiring each bilayer to scatter coherently rather than each monolayer. For DPPC, theta tilt was determined to be 32.0 +/- 0.5 degrees at 19 degrees C, slightly larger than previous direct determinations and considerably smaller than the value required by recent gravimetric measurements. This new value allows more accurate determinations of a variety of structural parameters, such as area per lipid molecule, A = 47.2 +/- 0.5 A2, and number of water molecules of hydration, nw = 11.8 +/- 0.7. As the chain length n of the lipids was increased from 16 to 20 carbons, the parameters A and nw remained constant, suggesting that the headgroup packing is at its excluded volume limit for this range. However, theta tilt increased by 3 degrees and the chain area Ac decreased by 0.5 A2. This behavior is explained in terms of a competition between a bulk free energy term and a finite or end effect term. Images FIGURE 6 FIGURE 7 PMID:8494973

Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids.

PubMed

Lau, King Hang Aaron; Sileika, Tadas S; Park, Sung Hyun; Sousa, Ana Maria Leal; Burch, Patrick; Szleifer, Igal; Messersmith, Phillip B

2015-01-07

Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevent non-specific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) "peptoids" are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platform for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with a different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs were found to give rise to distinct but subtle differences in properties. The results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.

Photolysis of nonylphenol ethoxylates: the determination of the degradation kinetics and the intermediate products.

PubMed

Chen, Ling; Zhou, Hai-Yun; Deng, Qin-Ying

2007-06-01

The photolysis of nonylphenol ethoxylates with an average oligomers length of ten ethoxylate units (NPEO(10)) in aqueous solution under UV, as well as the influence of humic acid (HA) on the photolysis was studied. A 125W high-pressure mercury lamp was employed as the light source. The intermediate products from the photolysis were determined by LC-MS. The results indicated that NPEO(10) underwent direct photolysis upon exposed to UV. The degradation pathway was complex. Besides the generally proposed degradation pathway of ethylene oxide (EO) side chains shortening, the oxidation of alkyl chain and EO chain led to intermediates having both a carboxylated (as well as carbonylated) ethoxylate and alkyl chain of varying lengths. The hydrogenation of benzene ring was also detected. The kinetics data showed that the first order reaction kinetics could be well used to describe the kinetics of NPEO(10) degradation. In the presence of dissolved organic matter by HA addition, the performance of NPEO(10) photodegradation was reduced. The photolysis rate decreased with increased HA concentration.

Interaction of cholesterol with sphingomyelins and acyl-chain-matched phosphatidylcholines: a comparative study of the effect of the chain length.

PubMed Central

Ramstedt, B; Slotte, J P

1999-01-01

In this study we have synthesized sphingomyelins (SM) and phosphatidylcholines (PC) with amide-linked or sn-2 linked acyl chains with lengths from 14 to 24 carbons. The purpose was to examine how the chain length and degree of unsaturation affected the interaction of cholesterol with these phospholipids in model membrane systems. Monolayers of saturated SMs and PCs with acyl chain lengths above 14 carbons were condensed and displayed a high collapse pressure ( approximately 70 mN/m). Monolayers of N-14:0-SM and 1(16:0)-2(14:0)-PC had a much lower collapse pressure (58-60 mN/m) and monounsaturated SMs collapsed at approximately 50 mN/m. The relative interaction of cholesterol with these phospholipids was determined at 22 degreesC by measuring the rate of cholesterol desorption from mixed monolayers (50 mol % cholesterol; 20 mN/m) to beta-cyclodextrin in the subphase (1.7 mM). The rate of cholesterol desorption was lower from saturated SM monolayers than from chain-matched PC monolayers. In SM monolayers, the rate of cholesterol desorption was very slow for all N-linked chains, whereas for PC monolayers we could observe higher desorption rates from monolayers of longer PCs. These results show that cholesterol interacts favorably with SMs (low rate of desorption), whereas its interaction (or miscibility) with long chain PCs is weaker. Introduction of a single cis-unsaturation in the N-linked acyl chain of SMs led to faster rates of cholesterol desorption as compared with saturated SMs. The exception was monolayers of N-22:1-SM and N-24:1-SM from which cholesterol desorbed almost as slowly as from the corresponding saturated SM monolayers. The results of this study suggest that cholesterol is most likely capable of interacting with all physiologically relevant (including long-chain) SMs present in the plasma membrane of cells. PMID:9929492

Structural propensities and entropy effects in peptide helix-coil transitions

NASA Astrophysics Data System (ADS)

Chemmama, Ilan E.; Pelea, Adam Colt; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2012-09-01

The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.

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

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele

We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

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

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele

X-ray diffraction and molecular dynamics simulations were used to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidinium ILsmore » increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. The results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

Dependence of Ion Dynamics on the Polymer Chain Length in Poly(ethylene oxide)-Based Polymer Electrolytes.

PubMed

Chattoraj, Joyjit; Knappe, Marisa; Heuer, Andreas

2015-06-04

It is known from experiments that in the polymer electrolyte system, which contains poly(ethylene oxide) chains (PEO), lithium-cations (Li(+)), and bis(trifluoromethanesulfonyl)imide-anions (TFSI(-)), the cation and the anion diffusion and the ionic conductivity exhibit a similar chain-length dependence: with increasing chain length, they start dropping steadily, and later, they saturate to constant values. These results are surprising because Li-cations are strongly correlated with the polymer chains, whereas TFSI-anions do not have such bonding. To understand this phenomenon, we perform molecular dynamics simulations of this system for four different polymer chain lengths. The diffusion results obtained from our simulations display excellent agreement with the experimental data. The cation transport model based on the Rouse dynamics can successfully quantify the Li-diffusion results, which correlates Li diffusion with the polymer center-of-mass motion and the polymer segmental motion. The ionic conductivity as a function of the chain length is then estimated based on the chain-length-dependent ion diffusion, which shows a temperature-dependent deviation for short chain lengths. We argue that in the first regime, counterion correlations modify the conductivity, whereas for the long chains, the system behaves as a strong electrolyte.

The role of discharge variation in scaling of drainage area and food chain length in rivers

USGS Publications Warehouse

Sabo, John L.; Finlay, Jacques C.; Kennedy, Theodore A.; Post, David M.

2010-01-01

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

The role of discharge variation in scaling of drainage area and food chain length in rivers.

PubMed

Sabo, John L; Finlay, Jacques C; Kennedy, Theodore; Post, David M

2010-11-12

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers

PubMed Central

Noriega, Rodrigo; Salleo, Alberto; Spakowitz, Andrew J.

2013-01-01

Existing models for the electronic properties of conjugated polymers do not capture the spatial arrangement of the disordered macromolecular chains over which charge transport occurs. Here, we present an analytical and computational description in which the morphology of individual polymer chains is dictated by well-known statistical models and the electronic coupling between units is determined using Marcus theory. The multiscale transport of charges in these materials (high mobility at short length scales, low mobility at long length scales) is naturally described with our framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational variability and spatial correlation. Our model offers a predictive approach to connecting processing conditions with transport behavior. PMID:24062459

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers.

PubMed

Noriega, Rodrigo; Salleo, Alberto; Spakowitz, Andrew J

2013-10-08

Existing models for the electronic properties of conjugated polymers do not capture the spatial arrangement of the disordered macromolecular chains over which charge transport occurs. Here, we present an analytical and computational description in which the morphology of individual polymer chains is dictated by well-known statistical models and the electronic coupling between units is determined using Marcus theory. The multiscale transport of charges in these materials (high mobility at short length scales, low mobility at long length scales) is naturally described with our framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational variability and spatial correlation. Our model offers a predictive approach to connecting processing conditions with transport behavior.

Impact of the alkyl chain length on binding of imidazolium-based ionic liquids to bovine serum albumin

NASA Astrophysics Data System (ADS)

Zhang, Mengyue; Wang, Ying; Zhang, Hongmei; Cao, Jian; Fei, Zhenghao; Wang, Yanqing

2018-05-01

The effects of six imidazolium-based ionic liquids (ILs) with different alkyl chain length ([CnMim]Cl, n = 2, 4, 6, 8, 10, 12) on the structure and functions of bovine serum albumin (BSA) were studied by multi-spectral methods and molecular docking. ILs with the longer alkyl chain length have the stronger binding interaction with BSA and the greater conformational damage to protein. The effects of ILs on the functional properties of BSA were further studied by the determination of non-enzyme esterase activity, β-fibrosis and other properties of BSA. The thermal stability of BSA was reduced, the rate of the formation of beta sheet structures of BSA was lowered, and the esterase-like activity of BSA were decreased with the increase of ILs concentration. Simultaneous molecular modeling technique revealed the favorable binding sites of ILs on protein. The hydrophobic force and polar interactions were the mainly binding forces of them. The calculated results are in a good agreement with the spectroscopic experiments. These studies on the impact of the alkyl chain length on binding of imidazolium-based ionic liquids to BSA are of great significance for understanding and developing the application of ionic liquid in life and physiological system.

Singular eigenstates in the even(odd) length Heisenberg spin chain

NASA Astrophysics Data System (ADS)

Ranjan Giri, Pulak; Deguchi, Tetsuo

2015-05-01

We study the implications of the regularization for the singular solutions on the even(odd) length spin-1/2 XXX chains in some specific down-spin sectors. In particular, the analytic expressions of the Bethe eigenstates for three down-spin sector have been obtained along with their numerical forms in some fixed length chains. For an even-length chain if the singular solutions \\{{{λ }α }\\} are invariant under the sign changes of their rapidities \\{{{λ }α }\\}=\\{-{{λ }α }\\}, then the Bethe ansatz equations are reduced to a system of (M-2)/2((M-3)/2) equations in an even (odd) down-spin sector. For an odd N length chain in the three down-spin sector, it has been analytically shown that there exist singular solutions in any finite length of the spin chain of the form N=3(2k+1) with k=1,2,3,\\cdots . It is also shown that there exist no singular solutions in the four down-spin sector for some odd-length spin-1/2 XXX chains.

Hydrodynamic radius fluctuations in model DNA-grafted nanoparticles

NASA Astrophysics Data System (ADS)

Vargas-Lara, Fernando; Starr, Francis W.; Douglas, Jack F.

2016-05-01

We utilize molecular dynamics simulations (MD) and the path-integration program ZENO to quantify hydrodynamic radius (Rh) fluctuations of spherical symmetric gold nanoparticles (NPs) decorated with single-stranded DNA chains (ssDNA). These results are relevant to understanding fluctuation-induced interactions among these NPs and macromolecules such as proteins. In particular, we explore the effect of varying the ssDNA-grafted NPs structural parameters, such as the chain length (L), chain persistence length (lp), NP core size (R), and the number of chains (N) attached to the nanoparticle core. We determine Rh fluctuations by calculating its standard deviation (σRh) of an ensemble of ssDNA-grafted NPs configurations generated by MD. For the parameter space explored in this manuscript, σR h shows a peak value as a function of N, the amplitude of which depends on L, lp and R, while the broadness depends on R.

Time-dependent effects of perfluorinated compounds on viability in cerebellar granule neurons: Dependence on carbon chain length and functional group attached.

PubMed

Berntsen, Hanne Friis; Bjørklund, Cesilie Granum; Audinot, Jean-Nicolas; Hofer, Tim; Verhaegen, Steven; Lentzen, Esther; Gutleb, Arno Christian; Ropstad, Erik

2017-12-01

The toxicity of long chained perfluoroalkyl acids (PFAAs) has previously been reported to be related to the length of the perfluorinated carbon chain and functional group attached. In the present study, we compared the cytotoxicity of six PFAAs, using primary cultures of rat cerebellar granule neurons (CGNs). Two perfluoroalkyl sulfonic acids (PFSAs, chain length C 6 and C 8 ) and four perfluoroalkyl carboxylic acids (PFCAs, chain length C 8 -C 11 ) were studied. These PFAAs have been detected in human blood and the brain tissue of mammals. The cell viability trypan blue and MTT assays were used to determine toxicity potencies (based on LC 50 values) after 24h exposure (in descending order): perfluoroundecanoic acid (PFUnDA)≥perfluorodecanoic acid (PFDA)>perfluorooctanesulfonic acid potassium salt (PFOS)>perfluorononanoic acid (PFNA)>perfluorooctanoic acid (PFOA)>perfluorohexanesulfonic acid potassium salt (PFHxS). Concentrations of the six PFAAs that produced equipotent effects after 24h exposure were used to further explore the dynamics of viability changes during this period. Therefore viability was assessed at 10, 30, 60, 90, 120 and 180min as well as 6, 12, 18 and 24h. A difference in the onset of reduction in viability was observed, occurring relatively quickly (30-60min) for PFOS, PFDA and PFUnDA, and much slower (12-24h) for PFHxS, PFOA and PFNA. A slight protective effect of vitamin E against PFOA, PFNA and PFOS-induced reduction in viability indicated a possible involvement of oxidative stress. PFOA and PFOS did not induce lipid peroxidation on their own, but significantly accelerated cumene hydroperoxide-induced lipid peroxidation. When distribution of the six PFAAs in the CGN-membrane was investigated using NanoSIMS50 imaging, two distinct patterns appeared. Whereas PFHxS, PFOS and PFUnDA aggregated in large hotspots, PFOA, PFNA and PFDA showed a more dispersed distribution pattern. In conclusion, the toxicity of the investigated PFAAs increased with increasing carbon chain length. For molecules with a similar chain length, a sulfonate functional group led to greater toxicity than a carboxyl group. Copyright © 2017 Elsevier B.V. All rights reserved.

The Snakelike Chain Character of Unstructured RNA

PubMed Central

Jacobson, David R.; McIntosh, Dustin B.; Saleh, Omar A.

2013-01-01

In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod “wormlike chain” (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a “snakelike chain,” characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation. PMID:24314087

Chlorinated paraffins wrapping of carbon nanotubes: A theoretical investigation

NASA Astrophysics Data System (ADS)

Ding, Qiuyue; Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence

2018-04-01

How nanomaterials interact with pollutants is the central for understanding their environmental behavior and practical application. In this work, molecular dynamics (MD) and density functional theoretical (DFT) methods were used to investigated the influence of carbon chain length, degree of chlorination, chain configuration, and chirality of chlorinated paraffin (CP) and diameter of single-walled carbon nanotubes (SWNTs) on the interaction between CPs and SWNTs. The simulation results demonstrated that CP chain length and chlorination degree played considerably important roles in determining interaction strength between SWNTs and CPs. The interaction energies increased with increasing chain length and chlorination degree. The chirality of SWNT exerted negligible influence on the interaction energy between SWNTs and CPs. On the contrary, interaction energy increased with increasing radius of SWNTs due to the surface curvatures. This result was rationalized by considering the decrease in SWNT curvature with increasing radius, which resulted in plane-like CNT wall. The negligible influence of CP chain configurations was attributed to relative flexibility of CP carbon chains, which can wrap on tubes through conformational changes with low-energy barriers. MD results indicated that CPs could adsorb on SWNT surface rapidly in aqueous environment. Charge transfer and electronic density results indicated that the interaction between CPs and SWNTs was physisorption in nature. This work provides fundamental information regarding SWNTs as sorbents for CPs extraction and adsorptive removal from environmental water system.

Influence of alkyl chain length compatibility on microemulsion structure and solubilization

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

Bansal, V.K.; O'Connell, J.P.; Shah, D.O.

1980-06-01

The water solubilization capacity of water/oil microemulsions is studied as a function of alkyl chain length of oil (C/sub 8/ to C/sub 16/), surfactant (C/sub 14/ and C/sub 18/ fatty acid soaps), and alcohol (C/sub 4/ to C/sub 7/). Sodium stearate and sodium myristate were used as surfactants. For n-butanol microemulsions the maximum amount of water solubilized in the microemulsion decreased continuously with increasing oil chain length; for n-heptanol it increased continuously. For n-pentanol and n-hexanol systems, water solubilization reached a maximum when the oil chain length plus alcohol chain length was equal to that of the surfactant. The electricmore » resistance and dielectric constant of the microemulsions also are measured as a function of alkyl chain length of the oil. 48 references.« less

The critical main-chain length for helix formation in water: determined in a peptide series with alternating Aib and Ala residues exclusively and detected with ECD spectroscopy.

PubMed

Longo, Edoardo; Moretto, Alessandro; Formaggio, Fernando; Toniolo, Claudio

2011-10-01

Critical main-chain length for peptide helix formation in the crystal (solid) state and in organic solvents has been already reported. In this short communication, we describe our results aiming at assessing the aforementioned parameter in water solution. To this goal, we synthesized step-by-step by solution procedures a complete series of N-terminally acetylated, C-terminally methoxylated oligopeptides, characterized only by alternating Aib and Ala residues, from the dimer to the nonamer level. All these compounds were investigated by electronic circular dichroism in the far-UV region in water solution as a function of chemical structure, namely presence/absence of an ester moiety or a negative charge at the C-terminus, and temperature. We find that the critical main-chain lengths for 3(10)- and α-helices, although still formed to a limited extent, in aqueous solution are six and eight residues, respectively. © 2011 Wiley-Liss, Inc.

Effect of diurnal photosynthetic activity on the fine structure of amylopectin from normal and waxy barley starch.

PubMed

Goldstein, Avi; Annor, George; Blennow, Andreas; Bertoft, Eric

2017-09-01

The impact of diurnal photosynthetic activity on the fine structure of the amylopectin fraction of starch synthesized by normal barley (NBS) and waxy barley (WBS), the latter completely devoid of amylose biosynthesis, was determined following the cultivation under normal diurnal or constant light growing conditions. The amylopectin fine structures were analysed by characterizing its unit chain length profiles after enzymatic debranching as well as its φ,β-limit dextrins and its clusters and building blocks after their partial and complete hydrolysis with α-amylase from Bacillus amyloliquefaciens, respectively. Regardless of lighting conditions, no structural effects were found when comparing both the amylopectin side-chain distribution and the internal chain fragments of these amylopectins. However, the diurnally grown NBS and WBS both showed larger amylopectin clusters and these had lower branching density and longer average chain lengths than clusters derived from plants grown under constant light conditions. Amylopectin clusters from diurnally grown plants also consisted of a greater number of building blocks, and shorter inter-block chain lengths compared to clusters derived from plants grown under constant light. Our data demonstrate that the diurnal light regime influences the fine structure of the amylopectin component both in amylose and non-amylose starch granules. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids

DOE PAGES

Lau, King Hang Aaron; Sileika, Tadas S.; Park, Sung Hyun; ...

2014-11-26

Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevents nonspecific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) “peptoids” are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platformmore » for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs are found to give rise to distinct but subtle differences in properties. In conclusion, the results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.« less

BCR CDR3 length distributions differ between blood and spleen and between old and young patients, and TCR distributions can be used to detect myelodysplastic syndrome

NASA Astrophysics Data System (ADS)

Pickman, Yishai; Dunn-Walters, Deborah; Mehr, Ramit

2013-10-01

Complementarity-determining region 3 (CDR3) is the most hyper-variable region in B cell receptor (BCR) and T cell receptor (TCR) genes, and the most critical structure in antigen recognition and thereby in determining the fates of developing and responding lymphocytes. There are millions of different TCR Vβ chain or BCR heavy chain CDR3 sequences in human blood. Even now, when high-throughput sequencing becomes widely used, CDR3 length distributions (also called spectratypes) are still a much quicker and cheaper method of assessing repertoire diversity. However, distribution complexity and the large amount of information per sample (e.g. 32 distributions of the TCRα chain, and 24 of TCRβ) calls for the use of machine learning tools for full exploration. We have examined the ability of supervised machine learning, which uses computational models to find hidden patterns in predefined biological groups, to analyze CDR3 length distributions from various sources, and distinguish between experimental groups. We found that (a) splenic BCR CDR3 length distributions are characterized by low standard deviations and few local maxima, compared to peripheral blood distributions; (b) healthy elderly people's BCR CDR3 length distributions can be distinguished from those of the young; and (c) a machine learning model based on TCR CDR3 distribution features can detect myelodysplastic syndrome with approximately 93% accuracy. Overall, we demonstrate that using supervised machine learning methods can contribute to our understanding of lymphocyte repertoire diversity.

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities

PubMed Central

Zhou, Han; Li, Fang; Weir, Michael D.; Xu, Hockin H.K.

2013-01-01

Objectives Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Methods Six QAMs were synthesized with CL = 3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond Multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL = 16) was mixed into SBMP at mass fraction = 0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4 hours. Biofilm colony-forming units (CFU) were measured at 2 days. Results Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL = 16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Conclusions Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. PMID:23948394

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities.

PubMed

Zhou, Han; Li, Fang; Weir, Michael D; Xu, Hockin H K

2013-11-01

Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Six QAMs were synthesized with CL=3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL=16) was mixed into SBMP at mass fraction=0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4h. Biofilm colony-forming units (CFU) were measured at 2 days. Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL=16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Side-Chain Effects on the Thermoelectric Properties of Fluorene-Based Copolymers.

PubMed

Liang, Ansheng; Zhou, Xiaoyan; Zhou, Wenqiao; Wan, Tao; Wang, Luhai; Pan, Chengjun; Wang, Lei

2017-09-01

Three conjugated polymers with alkyl chains of different lengths are designed and synthesized, and their structure-property relationship as organic thermoelectric materials is systematically elucidated. All three polymers show similar photophysical properties, thermal properties, and mechanical properties; however, their thermoelectric performance is influenced by the length of their side chains. The length of the alkyl chain significantly influences the electrical conductivity of the conjugated polymers, and polymers with a short alkyl chain exhibit better conductivity than those with a long alkyl chain. The length of the alkyl chain has little effect on the Seebeck coefficient. Only a slight increase in the Seebeck coefficient is observed with the increasing length of the alkyl chain. The purpose of this study is to provide comprehensive insight into fine-tuning the thermoelectric properties of conjugated polymers as a function of side-chain engineering, thereby providing a novel perspective into the design of high-performance thermoelectric conjugated polymers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymer chain alignment and transistor properties of nanochannel-templated poly(3-hexylthiophene) nanowires

NASA Astrophysics Data System (ADS)

Oh, Seungjun; Hayakawa, Ryoma; Pan, Chengjun; Sugiyasu, Kazunori; Wakayama, Yutaka

2016-08-01

Nanowires of semiconducting poly(3-hexylthiophene) (P3HT) were produced by a nanochannel-template technique. Polymer chain alignment in P3HT nanowires was investigated as a function of nanochannel widths (W) and polymer chain lengths (L). We found that the ratio between chain length and channel width (L/W) was a key parameter as regards promoting polymer chain alignment. Clear dichroism was observed in polarized ultraviolet-visible (UV-Vis) absorption spectra only at a ratio of approximately L/W = 2, indicating that the L/W ratio must be optimized to achieve uniaxial chain alignment in the nanochannel direction. We speculate that an appropriate L/W ratio is effective in confining the geometries and conformations of polymer chains. This discussion was supported by theoretical simulations based on molecular dynamics. That is, the geometry of the polymer chains, including the distance and tilting angles of the chains in relation to the nanochannel surface, was dominant in determining the longitudinal alignment along the nanochannels. Thus prepared highly aligned polymer nanowire is advantageous for electrical carrier transport and has great potential for improving the device performance of field-effect transistors. In fact, a one-order improvement in carrier mobility was observed in a P3HT nanowire transistor.

Opening of DNA chain due to force applied on different locations.

PubMed

Singh, Amar; Modi, Tushar; Singh, Navin

2016-09-01

We consider a homogeneous DNA molecule and investigate the effect of random force applied on the unzipping profile of the molecule. How the critical force varies as a function of the chain length or number of base pairs is the objective of this study. In general, the ratio of the critical forces that is applied on the middle of the chain to that which is applied on one of the ends is two. Our study shows that this ratio depends on the length of the chain. This means that the force which is applied to a point can be experienced by a section of the chain. Beyond a length, the base pairs have no information about the applied force. In the case when the chain length is shorter than this length, this ratio may vary. Only in the case when the chain length exceeds a critical length, this ratio is found to be two. Based on the de Gennes formulation, we developed a method to calculate these forces at zero temperature. The exact results at zero temperature match numerical calculations.

Electrostatic contribution to the persistence length of a semiflexible dipolar chain.

PubMed

Podgornik, Rudi

2004-09-01

We investigate the electrostatic contribution to the persistence length of a semiflexible polymer chain whose segments interact via a screened Debye-Hückel dipolar interaction potential. We derive the expressions for the renormalized persistence length on the level of a 1/D-expansion method already successfully used in other contexts of polyelectrolye physics. We investigate different limiting forms of the renormalized persistence length of the dipolar chain and show that, in, general, it depends less strongly on the screening length than in the context of a monopolar chain. We show that for a dipolar chain the electrostatic persistence length in the same regime of the parameter phase space as the original Odijk-Skolnick-Fixman (OSF) form for a monopolar chain depends logarithmically on the screening length rather than quadratically. This can be understood solely on the basis of a swifter decay of the dipolar interactions with separation compared to the monopolar electrostatic interactions. We comment also on the general contribution of higher multipoles to the electrostatic renormalization of the bending rigidity.

Effects of chain length, chlorination degree, and structure on the octanol-water partition coefficients of polychlorinated n-alkanes.

PubMed

Hilger, Bettina; Fromme, Hermann; Völkel, Wolfgang; Coelhan, Mehmet

2011-04-01

Log octanol-water partition coefficients (log Kow) of 40 synthesized polychlorinated n-alkanes (PCAs) with different chlorination degrees were determined using reversed-phase high performance liquid chromatography (RP-HPLC). In addition, log Kow values of a technical mixture namely Cereclor 63L as well as 15 individual in house synthesized C10, C11, and C12 chloroalkanes with known chlorine positions were estimated. Based on these results, the effects of chain length, chlorination degree, and structure were explored. The estimated log Kow values ranged from 4.10 (polychlorinated n-decanes with 50.2% chlorine content) to 11.34 (polychlorinated n-octacosanes with 54.8% chlorine content) for PCAs and from 3.82 (1,2,5,6,9,10-hexachlorodecane) to 7.75 (1,1,1,3,9,11,11,11-octachlorododecane) for the individual chloroalkanes studied. The results showed that log Kow value was influenced linearly at a given chlorine content by chain length, while a polynominal effect was observed in dependence on the chlorination degree of an alkane chain. Chlorine substitution pattern influenced markedly the log Kow value of chloroalkanes.

Affinity-reversed-phase liquid chromatography assay to quantitate recombinant antibodies and antibody fragments in fermentation broth.

PubMed

Battersby, J E; Snedecor, B; Chen, C; Champion, K M; Riddle, L; Vanderlaan, M

2001-08-24

An automated dual-column liquid chromatography assay comprised of affinity and reversed-phase separations that quantifies the majority of antibody-related protein species found in crude cell extracts of recombinant origin is described. Although potentially applicable to any antibody preparation, we here use samples of anti-CD18 (Fab'2LZ) and a full-length antibody, anti-tissue factor (anti-TF), from various stages throughout a biopharmaceutical production process to describe the assay details. The targeted proteins were captured on an affinity column containing an anti-light-chain (kappa) Fab antibody (AME5) immobilized on controlled pore glass. The affinity column was placed in-line with a reversed-phase column and the captured components were transferred by elution with dilute acid and subsequently resolved by eluting the reversed-phase column with a shallow acetonitrile gradient. Characterization of the resolved components showed that most antibody fragment preparations contained a light-chain fragment, free light chain, light-chain dimer and multiple forms of Fab'. Analysis of full-length antibody preparations also resolved these fragments as well as a completely assembled form. Co-eluting with the full-length antibody were high-molecular-mass variants that were missing one or both light chains. Resolved components were quantified by comparison with peak areas of similarly treated standards. By comparing the two-dimensional polyacrylamide gel electrophoresis patterns of an Escherichia coli blank run, a production run and the material affinity captured (AME5) from a production run, it was determined that the AME5 antibody captured isoforms of light chain, light chain covalently attached to heavy chain, and truncated light chain isoforms. These forms comprise the bulk of the soluble product-related fragments found in E. coli cell extracts of recombinantly produced antibody fragments.

The effect of elastomer chain length on properties of silicone-modified polyimide adhesives

NASA Technical Reports Server (NTRS)

St.clair, A. K.; St.clair, T. L.; Ezzell, S.

1981-01-01

A series of polyimides containing silicone elastomers was synthesized in order to study the effects of the elastomer chain length on polymer properties. The elastomer with repeat units varying from n=10 to 105 was chemically reacted into the backbone of an addition polyimide oligomer via reactive aromatic amine groups. Glass transition temperatures of the elastomer and polyimide phases were observed by torsional braid analysis. The elastomer-modified polyimides were tested as adhesives for bonding titanium in order to determine their potential for aerospace applications. Adhesive lap shear tests were performed before and after aging bonded specimens at elevated temperatures.

DNA compaction by poly (amido amine) dendrimers of ammonia cored and ethylene diamine cored

NASA Astrophysics Data System (ADS)

Qamhieh, K.; Al-Shawwa, J.

2017-06-01

The complexes build-up of DNA and soft particles poly amidoamine (PAMAM) dendrimers of ammonia cored of generations (G1-G6) and ethylenediamine cored of generations (G1-G10) have been studied, using a new theoretical model developed by Qamhieh and coworkers. The model describes the interaction between linear polyelectrolyte (LPE) chain and ion-penetrable spheres. Many factors affecting LPE/dendrimer complex have been investigated such as dendrimer generation, the Bjerrum length, salt concentration, and rigidity of the LPE chain represented by the persistence length. It is found that the wrapping chain length around dendrimer increases by increasing dendrimer`s generation, Bjerrum length, and salt concentration, while decreases by increasing the persistence length of the LPE chain. Also we can conclude that the wrapping length of LPE chain around ethylenediamine cored dendrimers is larger than its length around ammonia cored dendrimers.

Tunable evolutions of shock absorption and energy partitioning in magnetic granular chains

NASA Astrophysics Data System (ADS)

Leng, Dingxin; Liu, Guijie; Sun, Lingyu

2018-01-01

In this paper, we investigate the tunable characteristics of shock waves propagating in one-dimensional magnetic granular chains at various chain lengths and magnetic flux densities. According to the Hertz contact theory and Maxwell principle, a discrete element model with coupling elastic and field-induced interaction potentials of adjacent magnetic grains is proposed. We also present hard-sphere approximation analysis to describe the energy partitioning features of magnetic granular chains. The results demonstrate that, for a fixed magnetic field strength, when the chain length is greater than two times of the wave width of the solitary wave, the chain length has little effect on the output energy of the system; for a fixed chain length, the shock absorption and energy partitioning features of magnetic granular chains are remarkably influenced by varying magnetic flux densities. This study implies that the magnetic granular chain is potential to construct adaptive shock absorption components for impulse mitigation.

Conformation and stretching of end-tethered polymers in pressure-driven flow under confinement

NASA Astrophysics Data System (ADS)

Roy, Tamal; Hardt, Steffen; InstituteNano-; Microfludics, Technische Universität Darmstadt Team

2016-11-01

Understanding of the conformation and dynamics of polymers under confinement is important for both fundamental studies and applications. We experimentally study the conformation and stretching of surface-tethered polymer chains confined between parallel surfaces and exposed to a pressure-driven flow. λ-DNA molecules are tethered to the wall of a microchannel of height smaller than the contour lengths of the molecules. The DNA molecules, stained with a fluorescent dye, are visualized by epifluorescence and laser-scanning confocal microscopy (LSCM). The effects of the channel height, flow rate and contour length on the extension of the molecules are determined from epifluorescence images. From LSCM images the complete conformation and orientation of the DNA molecules is inferred. We find that the fractional extension of the molecules is uniquely determined by the fluid shear stress at the tethering surface and the chain contour length. There is no explicit influence of the channel height in the range of contour lengths we consider. We also derive analytical scaling relationships (in the weak and strong extension limits) that explain the experimentally observed stretching characteristics. This work is supported by Deutsche Forschungsgemeinschaft (Grant No. HA 2696/33-1).

Critical determinant of intestinal permeability and oral bioavailability of pegylated all trans-retinoic acid prodrug-based nanomicelles: Chain length of poly (ethylene glycol) corona.

PubMed

Li, Zhenbao; Han, Xiaopeng; Zhai, Yinglei; Lian, He; Zhang, Dong; Zhang, Wenjuan; Wang, Yongjun; He, Zhonggui; Liu, Zheng; Sun, Jin

2015-06-01

Pegylation method is widely used to prolong the blood circulation time of proteins and nanoparticles after intravenous administration, but the effect of surface poly (ethylene glycol) (PEG) chain length on oral absorption of the pegylated nanoparticles is poorly reported. The aim of our study was to investigate the influence of PEG corona chain length on membrane permeability and oral bioavailability of the amphiphilic pegylated prodrug-based nanomicelles, taking all trans-retinoic acid (ATRA) as a model drug. The amphiphilic ATRA-PEG conjugates were synthesized by esterification reaction between all trans-retinoic acid and mPEGs (mPEG500, mPEG1000, mPEG2000, and mPEG5000). The conjugates could self-assemble in aqueous medium to form nanomicelles by emulsion-solvent evaporation method. The resultant nanomicelles were in spherical shape with an average diameter of 13-20 nm. The drug loading efficiency of ATRA-PEG500, ATRA-PEG1000, ATRA-PEG2000, and ATRA-PEG5000 was about 38.4, 26.6, 13.1, and 5.68 wt%, respectively. With PEG chain length ranging from 500 to 5000, ATRA-PEG nanomicelles exhibited a bell shape of chemical stability in different pH buffers, intestinal homogenate and plasma. More importantly, they were all rapidly hydrolyzed into the parent drug in hepatic homogenate, with the half-time values being 0.3-0.4h. In comparison to ATRA solution and ATRA prodrug-based nanomicelles, ATRA-PEG1000 showed the highest intestinal permeability. After oral administration, ATRA-PEG2000 and ATRA-PEG5000 nanomicelles were not nearly absorbed, while the oral bioavailability of ATRA-PEG500 and ATRA-PEG1000 demonstrated about 1.2- and 2.0-fold higher than ATRA solution. Our results indicated that PEG1000 chain length of ATRA-PEG prodrug nanomicelles has the optimal oral bioavailability probably due to improved stability and balanced mucus penetration capability and cell binding, and that the PEG chain length on a surface of nanoparticles cannot exceed a key threshold with the purpose of enhancement in oral bioavailability. Copyright © 2015. Published by Elsevier B.V.

Mass spectrometric method to determine the chain length of oligosaccharides attached to phenolic polymers by nonglycosidic linkages

Treesearch

James L. Minor; Roger C. Pettersen

1987-01-01

In many plants, a portion of the polysaccharides appears to have a very low degree of cross-linking with aromatic polymers such as lignin or flavolans. The proportion of cross-linked units may be enriched for study by enzymatically hydrolyzing the nonbonded carbohydrates. A convenient method is described for the simultaneous analysis of sugar content and apparent chain...

Light-responsive expansion-contraction of spherical nanoparticle grafted with azopolymers

NASA Astrophysics Data System (ADS)

Fu, Jie; Zhang, Xinghua; Miao, Bing; Yan, Dadong

2017-04-01

Due to the very importance for both fundamental research and technological applications, smart materials with stimuli-responsive properties have been studied intensively. Theoretical investigation contributes to this endeavor through constructing and analyzing a model system which captures main features of the corresponding complex material, wherefrom useful insight can be provided to the trial-and-error experiments. We here report a theoretical study on the smart spherical nanoparticle grafted with light-responsive azobenzene-containing polymers. Utilizing the photoisomerization ability of the azobenzene group, nanoparticles can undergo a light-induced expansion-contraction transition. The wormlike chain based single chain in mean field theory, which has been developed by us recently, is used to investigate this transition in detail. Exploring a large parameter space, our results definitely determine the parameters, including the chain length and effective Kuhn length of grafted chain, nanoparticle radius, grafting density, and position of the azobenzene group along the chain contour, to admit optimum light-responsive behavior of the smart nanoparticle, which provides a guide for experimentalists to design this type of material in a rational manner.

Polymer Physics Prize Talk

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Polymer electrolytes have been particularly difficult to describe theoretically given the large number of disparate length scales involved in determining their physical properties. The Debye length, the Bjerrum length, the ion size, the chain length, and the distance between the charges along their backbones determine their structure and their response to external fields. We have developed an approach that uses multi-scale calculations with the capability of demonstrating the phase behavior of polymer electrolytes and of providing a conceptual understanding of how charge dictates nano-scale structure formation. Moreover, our molecular dynamics simulations have provided an understanding of the coupling of their conformation to their dynamics, which is crucial to design self-assembling materials, as well as to explore the dynamics of complex electrolytes for energy storage and conversion applications.

Topological analysis of polymeric melts: chain-length effects and fast-converging estimators for entanglement length.

PubMed

Hoy, Robert S; Foteinopoulou, Katerina; Kröger, Martin

2009-09-01

Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length N_{e} which operate on results for a single chain length N are shown to produce systematic O(1/N) errors. The mathematical roots of these errors are identified as (a) treating chain ends as entanglements and (b) neglecting non-Gaussian corrections to chain and primitive path dimensions. The prefactors for the O(1/N) errors may be large; in general their magnitude depends both on the polymer model and the method used to obtain primitive paths. We propose, derive, and test new estimators which eliminate these systematic errors using information obtainable from the variation in entanglement characteristics with chain length. The new estimators produce accurate results for N_{e} from marginally entangled systems. Formulas based on direct enumeration of entanglements appear to converge faster and are simpler to apply.

[Study of Determination of Oil Mixture Components Content Based on Quasi-Monte Carlo Method].

PubMed

Wang, Yu-tian; Xu, Jing; Liu, Xiao-fei; Chen, Meng-han; Wang, Shi-tao

2015-05-01

Gasoline, kerosene, diesel is processed by crude oil with different distillation range. The boiling range of gasoline is 35 ~205 °C. The boiling range of kerosene is 140~250 °C. And the boiling range of diesel is 180~370 °C. At the same time, the carbon chain length of differentmineral oil is different. The carbon chain-length of gasoline is within the scope of C7 to C11. The carbon chain length of kerosene is within the scope of C12 to C15. And the carbon chain length of diesel is within the scope of C15 to C18. The recognition and quantitative measurement of three kinds of mineral oil is based on different fluorescence spectrum formed in their different carbon number distribution characteristics. Mineral oil pollution occurs frequently, so monitoring mineral oil content in the ocean is very important. A new method of components content determination of spectra overlapping mineral oil mixture is proposed, with calculation of characteristic peak power integrationof three-dimensional fluorescence spectrum by using Quasi-Monte Carlo Method, combined with optimal algorithm solving optimum number of characteristic peak and range of integral region, solving nonlinear equations by using BFGS(a rank to two update method named after its inventor surname first letter, Boyden, Fletcher, Goldfarb and Shanno) method. Peak power accumulation of determined points in selected area is sensitive to small changes of fluorescence spectral line, so the measurement of small changes of component content is sensitive. At the same time, compared with the single point measurement, measurement sensitivity is improved by the decrease influence of random error due to the selection of points. Three-dimensional fluorescence spectra and fluorescence contour spectra of single mineral oil and the mixture are measured by taking kerosene, diesel and gasoline as research objects, with a single mineral oil regarded whole, not considered each mineral oil components. Six characteristic peaks are selected for characteristic peak power integration to determine components content of mineral oil mixture of gasoline, kerosene and diesel by optimal algorithm. Compared with single point measurement of peak method and mean method, measurement sensitivity is improved about 50 times. The implementation of high precision measurement of mixture components content of gasoline, kerosene and diesel provides a practical algorithm for components content direct determination of spectra overlapping mixture without chemical separation.

The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima).

PubMed

Wang, Kai; Wambugu, Peterson W; Zhang, Bin; Wu, Alex Chi; Henry, Robert J; Gilbert, Robert G

2015-09-20

The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Supramolecular recognition control of polyethylene glycol modified N-doped graphene quantum dots: tunable selectivity for alkali and alkaline-earth metal ions.

PubMed

Yang, Siwei; Sun, Jing; Zhu, Chong; He, Peng; Peng, Zheng; Ding, Guqiao

2016-02-07

The graphene quantum dot based fluorescent probe community needs unambiguous evidence about the control on the ion selectivity. In this paper, polyethylene glycol modified N-doped graphene quantum dots (PN-GQDs) were synthesized by alkylation reaction between graphene quantum dots and organic halides. We demonstrate the tunable selectivity and sensitivity by controlling the supramolecular recognition through the length and the end group size of the polyether chain on PN-GQDs. The relationship formulae between the selectivity/detection limit and polyether chains are experimentally deduced. The polyether chain length determines the interaction between the PN-GQDs and ions with different ratios of charge to radius, which in turn leads to a good selectivity control. Meanwhile the detection limit shows an exponential growth with the size of end groups of the polyether chain. The PN-GQDs can be used as ultrasensitive and selective fluorescent probes for Li(+), Na(+), K(+), Mg(2+), Ca(2+) and Sr(2+), respectively.

An equal force theory for network models of soft materials with arbitrary molecular weight distribution

NASA Astrophysics Data System (ADS)

Verron, E.; Gros, A.

2017-09-01

Most network models for soft materials, e.g. elastomers and gels, are dedicated to idealized materials: all chains admit the same number of Kuhn segments. Nevertheless, such standard models are not appropriate for materials involving multiple networks, and some specific constitutive equations devoted to these materials have been derived in the last few years. In nearly all cases, idealized networks of different chain lengths are assembled following an equal strain assumption; only few papers adopt an equal stress assumption, although some authors argue that such hypothesis would reflect the equilibrium of the different networks in contact. In this work, a full-network model with an arbitrary chain length distribution is derived by considering that chains of different lengths satisfy the equal force assumption in each direction of the unit sphere. The derivation is restricted to non-Gaussian freely jointed chains and to affine deformation of the sphere. Firstly, after a proper definition of the undeformed configuration of the network, we demonstrate that the equal force assumption leads to the equality of a normalized stretch in chains of different lengths. Secondly, we establish that the network with chain length distribution behaves as an idealized full-network of which both chain length and density of are provided by the chain length distribution. This approach is finally illustrated with two examples: the derivation of a new expression for the Young modulus of bimodal interpenetrated polymer networks, and the prediction of the change in fluorescence during deformation of mechanochemically responsive elastomers.

Acid diffusion, standing waves, and information theory: a molecular-scale model of chemically amplified resist

NASA Astrophysics Data System (ADS)

Trefonas, Peter, III; Allen, Mary T.

1992-06-01

Shannon's information theory is adapted to analyze the photolithographic process, defining the mask pattern as the prior state. Definitions and constraints to the general theory are developed so that the information content at various stages of the lithographic process can be described. Its application is illustrated by exploring the information content within projected aerial images and resultant latent images. Next, a 3-dimensional molecular scale model of exposure, acid diffusion, and catalytic crosslinking in acid-hardened resists (AHR) is presented. In this model, initial positions of photogenerated acids are determined by probability functions generated from the aerial images and the local light intensity in the film. In order to simulate post-exposure baking processes, acids are diffused in a random walk manner, for which the catalytic chain length and the average distance between crosslinks can be set. Crosslink locations are defined in terms of the topologically minimized number required to link different chains. The size and location of polymer chains involved in a larger scale crosslinked network is established and related to polymer solubility. In this manner, the nature of the crosslinked latent image can be established. Good correlation with experimental data is found for the calculated percent insolubilization as a function of dose when the rms acid diffusion length is about 500 angstroms. Information analysis is applied in detail to the specific example of AHR chemistry. The information contained within the 3-D crosslinked latent image is explored as a function of exposure dose, catalytic chain length, average distance between crosslinks. Eopt (the exposure dose which optimizes the information contained within the latent image) was found to vary with catalytic chain length in a manner similar to that observed experimentally in a plot of E90 versus post-exposure bake time. Surprisingly, the information content of the crosslinked latent image remains high even when rms diffusion lengths are as long as 1500 angstroms. The information content of a standing wave is shown to decrease with increasing diffusion length, with essentially all standing wave information being lost at diffusion lengths greater than 450 angstroms. A unique mechanism for self-contrast enhancement and high resolution in AHR resist is proposed.

Knotting probability of a shaken ball-chain.

PubMed

Hickford, J; Jones, R; du Pont, S Courrech; Eggers, J

2006-11-01

We study the formation of knots on a macroscopic ball chain, which is shaken on a horizontal plate at 12 times the acceleration of gravity. We find that above a certain critical length, the knotting probability is independent of chain length, while the time to shake out a knot increases rapidly with chain length. The probability of finding a knot after a certain time is the result of the balance of these two processes. In particular, the knotting probability tends to a constant for long chains.

Certain Chemical Substances Containing Varying Carbon Chain Lengths (Alkyl Ranges Using the Cx-y Notation) on the TSCA Inventory

EPA Pesticide Factsheets

This paper explains the conventions that are applied to certain listings of chemical substances containing ranges of alkyl chain lengths (i.e., carbon chains of varying lengths) for chemical substances on the Toxic Substances Control Act (TSCA)

Fracture Behavior in Nylon 6 Fibers. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lloyd, B. A.

1972-01-01

Electron paramagnetic resonance (EPR) techniques are used to determine the number of free radicals produced during deformation leading to fracture of nylon 6 fibers. A reaction rate molecular model is proposed to explain some of the deformation and bond rupture behavior leading to fracture. High-strength polymer fibers are assumed to consist of a sandwich structure of disordered and ordered regions along the fiber axis. In the disordered or critical flaw regions, tie chains connecting the ordered or crystalline block regions are assumed to have a statistical distribution in length. These chains are, therefore, subjected to different stresses. The effective length distribution was determined by EPR. The probability of bond rupture was assumed to be controlled by reaction-rate theory with a stress-aided activation energy and behavior of various loadings determined by numerical techniques. The model is successfully correlated with experimental stress, strain, and bond rupture results for creep, constant rate loadings, cyclic stress, stress relaxation and step strain tests at room temperature.

Self-Consistency of the Lauritzen-Hoffman and Strobl Models of Polymer Crystallization Evaluated for Poly(epsilon-caprolactone) Fractions and Effect of Composition on the Phenomenon of Concurrent Crystallization in Polyethylene Blends

NASA Astrophysics Data System (ADS)

Sheth, Swapnil Suhas

Narrow molecular weight fractions of poly(epsilon-caprolactone) were successfully obtained using the successive precipitation fractionation technique with toluene/n-heptane as a solvent/nonsolvent pair. Calorimetric studies of the melting behavior of fractions that were crystallized either isothermally or under constant cooling rate conditions suggested that the isothermal crystallization of the samples should be used for a proper evaluation of the molecular weight dependence of the observed melting temperature and degree of crystallinity in PCL. The molecular weight and temperature dependence of the spherulitic growth rate of fractions was studied in the context of the Lauritzen-Hoffman two-phase model and the Strobl three-phase model of polymer crystallization. The zero-growth rate temperatures, determined from spherulitic growth rates using four different methods, are consistent with each other and increase with chain length. The concomitant increase in the apparent secondary nucleation constant was attributed to two factors. First, for longer chains there is an increase in the probability that crystalline stems belong to loose chain-folds, hence, an increase in fold surface free energy. It is speculated that the increase in loose folding and resulting decrease in crystallinity with increasing chain length are associated with the ester group registration requirement in PCL crystals. The second contribution to the apparent nucleation constant arises from chain friction associated with segmental transport across the melt/crystal interface. These factors were responsible for the much stronger chain length dependence of spherulitic growth rates at fixed undercooling observed here with PCL than previously reported for PE and PEO. In the case of PCL, the scaling exponent associated with the chain length dependence of spherulitic growth rates exceeds the upper theoretical bound of 2 predicted from the Brochard- DeGennes chain pullout model. Observation that zero-growth and equilibrium melting temperature values are identical with each other within the uncertainty of their determinations casts serious doubt on the validity of Strobl three-phase model. A novel method is proposed to determine the Porod constant necessary to extrapolate the small angle X-ray scattering intensity data to large scattering vectors. The one-dimensional correlation function determined using this Porod constant yielded the values of lamellar crystal thickness, which were similar to these estimated using the Hosemann-Bagchi Paracrystalline Lattice model. The temperature dependence of the lamellar crystal thickness was consistent with both LH and the Strobl model of polymer crystallization. However, in contrast to the predictions of Strobl's model, the value of the mesomorph-to-crystal equilibrium transition temperature was very close to the zero-growth temperature. Moreover, the lateral block sizes (obtained using wide angle X-ray diffraction) and the lamellar thicknesses were not found to be controlled by the mesomorph-to-crystal equilibrium transition temperature. Hence, we concluded that the crystallization of PCL is not mediated by a mesophase. Metallocene-catalyzed linear low-density (m-LLDPE with 3.4 mol% 1-octene) and conventional low-density (LDPE) polyethylene blends of different compositions were investigated for their melt-state miscibility and concurrent crystallization tendency. Differential scanning calorimetric studies and morphological studies using atomic force microscopy confirm that these blends are miscible in the melt-state for all compositions. LDPE chains are found to crystallize concurrently with m-LLDPE chains during cooling in the m-LLDPE crystallization temperature range. While the extent of concurrent crystallization was found to be optimal in .. .. iv blends with highest m-LLDPE content studied, strong evidence was uncovered for the existence of a saturation effect in the concurrent crystallization behavior. This observation leads us to suggest that co-crystallization, rather than mere concurrent crystallization, of LDPE with m- LLDPE can indeed take place. Matching of the respective sequence length distributions in LDPE and m-LLDPE is suggested to control the extent of co-crystallization.

Synthesis, characterisation and physicochemical properties of hydrophobically modified inulin using long-chain fatty acyl chlorides.

PubMed

Han, Lingyu; Ratcliffe, I; Williams, P A

2017-12-15

A series of inulin derivatives were synthesized in aqueous solution using acyl chlorides with varying alkyl chain length (C10-C16). They were characterised using a number of techniques including MALDI TOF-MS, 1 H NMR and FTIR and their degree of substitution determined. The solution properties of the hydrophobically modified inulins were investigated using dye solubilisation and surface tension and it was confirmed that the molecules aggregated in solution above a critical concentration (critical aggregation concentration, CAC). The value of the CAC was found to be reasonably consistent between the different techniques and was shown to decrease with increasing hydrophobe chain length. It was found that the C10, C12 and C14 derivatives formed stable oil-in-water emulsions and the emulsion droplet size decreased with increasing alkyl chain length. The C16 derivative was not able to produce stable oil-in-water emulsions; however, it was able to form stable water-in-oil emulsions. The fact that the derivatives are able to form micellar-like aggregates and stabilise emulsions makes them suitable candidates for the encapsulation and delivery of active compounds with potential application in food, cosmetic, personal care and pharmaceutical formulations. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Concentration-Dependent Insulin Immobilization Behavior of Alkyl-Modified Silica Vesicles: The Impact of Alkyl Chain Length.

PubMed

Zhang, Jun; Zhang, Long; Lei, Chang; Huang, Xiaodan; Yang, Yannan; Yu, Chengzhong

2018-05-01

The insulin immobilization behaviors of silica vesicles (SV) before and after modification with hydrophobic alkyl -C 8 and -C 18 groups have been studied and correlated to the grafted alkyl chain length. In order to minimize the influence from the other structural parameters, monolayered -C 8 or -C 18 groups are grafted onto SV with controlled density. The insulin immobilization capacity of SV is dependent on the initial insulin concentrations (IIC). At high IIC (2.6-3.0 mg/mL), the trend of insulin immobilization capacity of SV is SV-OH > SV-C 8 > SV-C 18 , which is determined mainly by the surface area of SV. At medium IIC (0.6-1.9 mg/mL), the trend changes to SV-C 8 ≥ SV-C 18 > SV-OH as both the surface area and alkyl chain length contribute to the insulin immobilization. At an extremely low IIC, the hydrophobic-hydrophobic interaction between the alkyl group and insulin molecules plays the most significant role. Consequently, SV-C 18 with longer alkyl groups and the highest hydrophobicity show the best insulin enrichment performance compared to SV-C 8 and SV-OH, as evidenced by an insulin detection limit of 0.001 ng/mL in phosphate buffered saline (PBS) and 0.05 ng/mL in artficial urine determined by mass spectrometry (MS).

Modeling and self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution

NASA Astrophysics Data System (ADS)

Wu, Xiaohan; Li, Suming; Coumes, Fanny; Darcos, Vincent; Lai Kee Him, Joséphine; Bron, Patrick

2013-09-01

A series of poly(ethylene glycol)-polylactide-poly(ethylene glycol) (PEG-PLA-PEG) triblock copolymers with symmetric or asymmetric chain structures were synthesized by combination of ring-opening polymerization and copper-catalyzed click chemistry. The resulting copolymers were used to prepare self-assembled aggregates by dialysis. Various architectures such as nanotubes, polymersomes and spherical micelles were observed from transmission electron microscopy (TEM), cryo-TEM and atomic force microscopy (AFM) measurements. The formation of diverse aggregates is explained by modeling from the angle of both geometry and thermodynamics. From the angle of geometry, a ``blob'' model based on the Daoud-Cotton model for star polymers is proposed to describe the aggregate structures and structural changes with copolymer composition and molar mass. In fact, the copolymer chains extend in aqueous medium to form single layer polymersomes to minimize the system's free energy if one of the two PEG blocks is short enough. The curvature of polymersomes is dependent on the chain structure of copolymers, especially on the length of PLA blocks. A constant branch number of aggregates (f) is thus required to preserve the morphology of polymersomes. Meanwhile, the aggregation number (Nagg) determined from the thermodynamics of self-assembly is roughly proportional to the total length of polymer chains. Comparing f to Nagg, the aggregates take the form of polymersomes if Nagg ~ f, and change to nanotubes if Nagg > f to conform to the limits from both curvature and aggregation number. The length of nanotubes is mainly determined by the difference between Nagg and f. However, the hollow structure becomes unstable when both PEG segments are too long, and the aggregates eventually collapse to yield spherical micelles. Therefore, this work gives new insights into the self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution which present great interest for biomedical and pharmaceutical applications.A series of poly(ethylene glycol)-polylactide-poly(ethylene glycol) (PEG-PLA-PEG) triblock copolymers with symmetric or asymmetric chain structures were synthesized by combination of ring-opening polymerization and copper-catalyzed click chemistry. The resulting copolymers were used to prepare self-assembled aggregates by dialysis. Various architectures such as nanotubes, polymersomes and spherical micelles were observed from transmission electron microscopy (TEM), cryo-TEM and atomic force microscopy (AFM) measurements. The formation of diverse aggregates is explained by modeling from the angle of both geometry and thermodynamics. From the angle of geometry, a ``blob'' model based on the Daoud-Cotton model for star polymers is proposed to describe the aggregate structures and structural changes with copolymer composition and molar mass. In fact, the copolymer chains extend in aqueous medium to form single layer polymersomes to minimize the system's free energy if one of the two PEG blocks is short enough. The curvature of polymersomes is dependent on the chain structure of copolymers, especially on the length of PLA blocks. A constant branch number of aggregates (f) is thus required to preserve the morphology of polymersomes. Meanwhile, the aggregation number (Nagg) determined from the thermodynamics of self-assembly is roughly proportional to the total length of polymer chains. Comparing f to Nagg, the aggregates take the form of polymersomes if Nagg ~ f, and change to nanotubes if Nagg > f to conform to the limits from both curvature and aggregation number. The length of nanotubes is mainly determined by the difference between Nagg and f. However, the hollow structure becomes unstable when both PEG segments are too long, and the aggregates eventually collapse to yield spherical micelles. Therefore, this work gives new insights into the self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution which present great interest for biomedical and pharmaceutical applications. Electronic supplementary information (ESI) available: 1H-NMR, DOSY, FTIR, and GPC measurements, methods and results of the copolymers in PEG-PLA-PEG synthesis. See DOI: 10.1039/c3nr02899b

Structures and Optical Properties of Hydrazones Derived from Biological Polyenes

NASA Astrophysics Data System (ADS)

Nakashima, Takayasu; Yamada, Takashi; Hashimoto, Hideki; Kobayashi, Takayoshi

2001-08-01

A set of hydrazone molecules was derived from a series of biological polyenes that have different polyene chain-lengths with common substituent group of 2,4-dinitrophenylhydrazine. Their structures were determined by high-resolution NMR spectroscopy as well as X-ray crystallography, and their optical properties were investigated by room and low temperature optical absorption spectroscopy. Among the derivatives so far synthesized, the one that has the shortest polyene chain (C13-DNPH) afforded single crystals without inversion symmetry, hence applicable for the second-order nonlinear optical devices. Molecular structures in the crystals were closely inspected in order to explain the cause to violate the inversion symmetry. Hydrazones derived in this study gave rise to two transition moments along the molecular axis. Comparison of the optical absorption spectra among the derivatives showed a unique phenomenon that could be attributed to the crossover of the excited state potential energy surfaces along the elongation of the polyene chain-lengths.

Structures and Optical Properties of Hydrazones Derived from Biological Polyenes

NASA Astrophysics Data System (ADS)

Nakashima, Takayasu; Yamada, Takashi; Hashimoto, Hideki; Kobayashi, Takayoshi

A set of hydrazone molecules was derived from a series of biological polyenes that have different polyene chain-lengths with common substituent group of 2,4-dinitrophenylhydrazine. Their structures were determined by high-resolution NMR spectroscopy as well as X-ray crystallography, and their optical properties were investigated by room and low temperature optical absorption spectroscopy. Among the derivatives so far synthesized, the one that has the shortest polyene chain (C13-DNPH) afforded single crystals without inversion symmetry, hence applicable for the second-order nonlinear optical devices. Molecular structures in the crystals were closely inspected in order to explain the cause to violate the inversion symmetry. Hydrazones derived in this study gave rise to two transition moments along the molecular axis. Comparison of the optical absorption spectra among the derivatives showed a unique phenomenon that could be attributed to the crossover of the excited state potential energy surfaces along the elongation of the polyene chain-lengths.

Rouse mode analysis of chain relaxation in homopolymer melts

DOE PAGES

Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; ...

2014-09-15

We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inverselymore » with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.« less

Perfluorinated Surfactant Chain-Length Effects on Sonochemical Kinetics

NASA Astrophysics Data System (ADS)

Campbell, Tammy Y.; Vecitis, Chad D.; Mader, Brian T.; Hoffmann, Michael R.

2009-08-01

The sonochemical degradation kinetics of the aqueous perfluorochemicals (PFCs) perfluorobutanoate (PFBA), perfluorobutanesulfonate (PFBS), perfluorohexanoate (PFHA), and perfluorohexanesulfonate (PFHS) have been investigated. Surface tension measurements were used to evaluate chain-length effects on equilibrium air-water interface partitioning. The PFC air-water interface partitioning coefficients, KeqPF, and maximum surface concentrations, ΓmaxPF, were determined from the surface pressure equation of state for PFBA, PFBS, PFHA, and PFHS. Relative KeqPF values were dependent upon chain length KeqPFHS ≅ 2.1KeqPFHA ≅ 3.9KeqPFBS ≅ 5.0KeqPFBA, whereas relative ΓmaxPF values had minimal chain length dependence ΓmaxPFHS ≅ ΓmaxPFHA ≅ ΓmaxPFBS ≅ 2.2ΓmaxPFBA. The rates of sonolytic degradation were determined over a range of frequencies from 202 to 1060 kHz at dilute (<1 μM) initial PFC concentrations and are compared to previously reported results for their C8 analogs: perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA). Under all conditions, the time-dependent PFC sonolytic degradation was observed to follow pseudo-first-order kinetics, i.e., below kinetic saturation, suggesting bubble-water interface populations were significantly below the adsorption maximum. The PFHX (where X = A or S) sonolysis rate constant was observed to peak at an ultrasonic frequency of 358 kHz, similar to that for PFOX. In contrast, the PFBX degradation rate constants had an apparent maximum at 610 kHz. Degradation rates observed for PFHX are similar to previously determined PFOX rates, kapp,358PFOX ≅ kapp,358PFHX. PFOX is sonolytically pyrolyzed at the transiently cavitating bubble-water interface, suggesting that rates should be proportional to equilibrium interfacial partitioning. However, relative equilibrium air-water interfacial partitioning predicts that KeqPFOX ≅ 5KeqPFHX. This suggests that at dilute PFC concentrations, adsorption to the bubble-water interface is ultrasonically enhanced due to high-velocity radial bubble oscillations. PFC sonochemical kinetics are slower for PFBS and further diminished for PFBA as compared to longer analogs, suggesting that PFBX surface films are of lower stability due to their greater water solubility.

Kidney transplant chains amplify benefit of nondirected donors.

PubMed

Melcher, Marc L; Veale, Jeffrey L; Javaid, Basit; Leeser, David B; Davis, Connie L; Hil, Garet; Milner, John E

2013-02-01

Despite the potential for altruistic nondirected donors (NDDs) to trigger multiple transplants through nonsimultaneous transplant chains, concerns exist that these chains siphon NDDs from the deceased donor wait list and that donors within chains might not donate after their partner receives a transplant. To determine the number of transplantations NDDs trigger through chains. Retrospective review of large, multicenter living donor-recipient database. Fifty-seven US transplant centers contributing donor-recipient pairs to the database. The NDDs initiating chain transplantation. Number of transplants per NDD. Seventy-seven NDDs enabled 373 transplantations during 46 months starting February 2008. Mean chain length initiated by NDDs was 4.8 transplants (median, 3; range, 1-30). The 40 blood type O NDDs triggered a mean chain length of 6.0 (median, 4; range, 2-30). During the interval, 66 of 77 chains were closed to the wait list, 4 of 77 were ongoing, and 7 of 77 were broken because bridge donors became unavailable. No chains were broken in the last 15 months, and every recipient whose incompatible donor donated received a kidney. One hundred thirty-three blood type O recipients were transplanted. This large series demonstrates that NDDs trigger almost 5 transplants on average, more if the NDD is blood type O. There were more blood type O recipients than blood type O NDDs participating. The benefits of transplanting 373 patients and enabling others without living donors to advance outweigh the risk of broken chains that is decreasing with experience. Even 66 patients on the wait list without living donors underwent transplantation with living-donor grafts at the end of these chains.

Rapid Quantification of Low-Viscosity Acetyl-Triacylglycerols Using Electrospray Ionization Mass Spectrometry.

PubMed

Bansal, Sunil; Durrett, Timothy P

2016-09-01

Acetyl-triacylglycerols (acetyl-TAG) possess an sn-3 acetate group, which confers useful chemical and physical properties to these unusual triacylglycerols (TAG). Current methods for quantification of acetyl-TAG are time consuming and do not provide any information on the molecular species profile. Electrospray ionization mass spectrometry (ESI-MS)-based methods can overcome these drawbacks. However, the ESI-MS signal intensity for TAG depends on the aliphatic chain length and unsaturation index of the molecule. Therefore response factors for different molecular species need to be determined before any quantification. The effects of the chain length and the number of double-bonds of the sn-1/2 acyl groups on the signal intensity for the neutral loss of short chain length sn-3 groups were quantified using a series of synthesized sn-3 specific structured TAG. The signal intensity for the neutral loss of the sn-3 acyl group was found to negatively correlated with the aliphatic chain length and unsaturation index of the sn-1/2 acyl groups. The signal intensity of the neutral loss of the sn-3 acyl group was also negatively correlated with the size of that chain. Further, the position of the group undergoing neutral loss was also important, with the signal from an sn-2 acyl group much lower than that from one located at sn-3. Response factors obtained from these analyses were used to develop a method for the absolute quantification of acetyl-TAG. The increased sensitivity of this ESI-MS-based approach allowed successful quantification of acetyl-TAG in various biological settings, including the products of in vitro enzyme activity assays.

Structure of flexible and semiflexible polyelectrolyte chains in confined spaces of slit micro/nanochannels.

PubMed

Jeon, Jonggu; Chun, Myung-Suk

2007-04-21

Understanding the behavior of a polyelectrolyte in confined spaces has direct relevance in design and manipulation of microfluidic devices, as well as transport in living organisms. In this paper, a coarse-grained model of anionic semiflexible polyelectrolyte is applied, and its structure and dynamics are fully examined with Brownian dynamics (BD) simulations both in bulk solution and under confinement between two negatively charged parallel plates. The modeling is based on the nonlinear bead-spring discretization of a continuous chain with additional long-range electrostatic, Lennard-Jones, and hydrodynamic interactions between pairs of beads. The authors also consider the steric and electrostatic interactions between the bead and the confining wall. Relevant model parameters are determined from experimental rheology data on the anionic polysaccharide xanthan reported previously. For comparison, both flexible and semiflexible models are developed accompanying zero and finite intrinsic persistence lengths, respectively. The conformational changes of the polyelectrolyte chain induced by confinements and their dependence on the screening effect of the electrolyte solution are faithfully characterized with BD simulations. Depending on the intrinsic rigidity and the medium ionic strength, the polyelectrolyte can be classified as flexible, semiflexible, or rigid. Confined flexible and semiflexible chains exhibit a nonmonotonic variation in size, as measured by the radius of gyration and end-to-end distance, with changing slit width. For the semiflexible chain, this is coupled to the variations in long-range bond vector correlation. The rigid chain, realized at low ionic strength, does not have minima in size but exhibits a sigmoidal transition. The size of confined semiflexible and rigid polyelectrolytes can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at long length scale.

Asymptotic study of pulsating evolution of overdriven and CJ detonation with a chain-branching kinetics model

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

Short, Mark; Chliquete, Carlos

2011-01-20

The pulsating dynamics of gaseous detonations with a model two-step chain-branching kinetic mechanism are studied both numerically and asymptotically. The model studied here was also used in [4], [3] and [2] and mimics the attributes of some chain-branching reaction mechanisms. Specifically, the model comprises a chain-initiationlbranching zone with an Arrhenius temperature-sensitive rate behind the detonation shock where fuel is converted into chain-radical with no heat release. This is followed by a chain-termination zone having a temperature insensitive rate where the exothermic heat of reaction is released. The lengths of these two zones depend on the relative rates of each stage.more » It was determined in [4] and [3] via asymptotic and numerical analysis that the ratio of the length of the chain-branching zone to that of the chain-initation zone relative to the size of the von Neumann state scaled activation energy in the chain initiation/branching zone has a primary influence of the stability of one-dimensional pulsating instability behavior for this model. In [2], the notion of a specific stability parameter related to this ratio was proposed that determines the boundary between stable and unstable waves. In [4], a slow-time varying asymptotic study was conducted of pulsating instability of Chapman-Jouguet (CJ) detonations with the above two-step rate model, assuming a large activation energy for the chain-initiation zone and a chain-termination zone longer than the chain-initiation zone. Deviations D{sub n}{sup (1)} ({tau}) of the detonation velocity from Chapman-Jouguet were of the order of the non-dimensional activation energy. Solutions were sought for a pulsation timescale of the order of the non-dimensional activation energy times the particle transit time through the induction zone. On this time-scale, the evolution of the chain-initation zone is quasi-steady. In [4], a time-dependent non-linear evolution equation for D{sub n}{sup (1)} ({tau}) was then constructed via a perturbation procedure for cases where the ratio of the length of the chain-termination zone to chain-initiation zone was less than the non-dimensional activation energy. To leading order, the steady CJ detonation was found to be unstable; higher-order corrections lead to the construction of a stability limit between stable and unsteady pulsating solutions. One conclusion from this study is that for a stability limit to occur at leading order, the period of pulsation of the detonation must occur on the time scale of particle passage through the longer chain-termination zone, while the length of the chain-termination zone must be of order of the non-dimensional activation energy longer than the chain-initiation zone. The relevance of these suggested scalings was verified via numerical solutions of the full Euler system in [3], and formed the basis of the stability parameter criteria suggested in [2]. In the following, we formulate an asymptotic study based on these new suggested scales, studying the implications for describing pulsating behavior in gaseous chain-branching detonations. Specifically, we find that the chain-induction zone structure is the same as that studied in [4]. However, the study of unsteady evolution in the chain-termination region is now governed by a set of asymptotically derived nonlinear POEs. Equations for the linear stablity behavior of this set of POE's is obtained, while the nonlinear POEs are solved numerically using a shock-attached, shock-fitting method developed by Henrick et aJ. [1]. The results thus far show that the stability threshold calculated using the new ratio of the chain-termination zone length to that of the chain-initiation zone yields a marked improvement over [2]. Additionally, solutions will be compared with predictions obtained from the solution of the full Euler system. Finally, the evolution equation previously derived in [4] has been generalized to consider both arbitrary reaction orders and any degree of overdrive.« less

Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-β (iPLAβ)-mediated Glycerophospholipid Hydrolysis*

PubMed Central

Batchu, Krishna Chaithanya; Hokynar, Kati; Jeltsch, Michael; Mattonet, Kenny; Somerharju, Pentti

2015-01-01

The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca2+-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated. PMID:25713085

Free fatty acids chain length distribution affects the permeability of skin lipid model membranes.

PubMed

Uchiyama, Masayuki; Oguri, Masashi; Mojumdar, Enamul H; Gooris, Gert S; Bouwstra, Joke A

2016-09-01

The lipid matrix in the stratum corneum (SC) plays an important role in the barrier function of the skin. The main lipid classes in this lipid matrix are ceramides (CERs), cholesterol (CHOL) and free fatty acids (FFAs). The aim of this study was to determine whether a variation in CER subclass composition and chain length distribution of FFAs affect the permeability of this matrix. To examine this, we make use of lipid model membranes, referred to as stratum corneum substitute (SCS). We prepared SCS containing i) single CER subclass with either a single FFA or a mixture of FFAs and CHOL, or ii) a mixture of various CER subclasses with either a single FFA or a mixture of FFAs and CHOL. In vitro permeation studies were performed using ethyl-p-aminobenzoic acid (E-PABA) as a model drug. The flux of E-PABA across the SCS containing the mixture of FFAs was higher than that across the SCS containing a single FA with a chain length of 24 C atoms (FA C24), while the E-PABA flux was not effected by the CER composition. To select the underlying factors for the changes in permeability, the SCSs were examined by Fourier transform infrared spectroscopy (FTIR) and Small angle X-ray scattering (SAXS). All lipid models demonstrated a similar phase behavior. However, when focusing on the conformational ordering of the individual FFA chains, the shorter chain FFA (with a chain length of 16, 18 or 20 C atoms forming only 11m/m% of the total FFA level) had a higher conformational disordering, while the conformational ordering of the chains of the CER and FA C24 and FA C22 hardly did not change irrespective of the composition of the SCS. In conclusion, the conformational mobility of the short chain FFAs present only at low levels in the model SC lipid membranes has a great impact on the permeability of E-PABA. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of chain length on binding of fatty acids to Pluronics in microemulsions.

PubMed

James-Smith, Monica A; Shekhawat, Dushyant; Cheung, Sally; Moudgil, Brij M; Shah, Dinesh O

2008-03-15

We investigated the effect of fatty acid chain length on the binding capacity of drug and fatty acid to Pluronic F127-based microemulsions. This was accomplished by using turbidity experiments. Pluronic-based oil-in-water microemulsions of various compositions were synthesized and titrated to turbidity with concentrated Amitriptyline, an antidepressant drug. Sodium salts of C(8), C(10), or C(12) fatty acid were used in preparation of the microemulsion and the corresponding binding capacities were observed. It has been previously determined that, for microemulsions prepared with sodium caprylate (C(8) fatty acid soap), a maximum of 11 fatty acid molecules bind to the microemulsion per 1 molecule of Pluronic F127 and a maximum of 12 molecules of Amitriptyline bind per molecule of F127. We have found that with increasing the chain length of the fatty acid salt component of the microemulsion, the binding capacity of both the fatty acid and the Amitriptyline to the microemulsion decreases. For sodium salts of C(8), C(10) and C(12) fatty acids, respectively, a maximum of approximately 11, 8.4 and 8.3 molecules of fatty acid molecules bind to 1 Pluronic F127 molecule. We propose that this is due to the decreasing number of free monomers with increasing chain length. As chain length increases, the critical micelle concentration (cmc) decreases, thus leading to fewer monomers. Pluronics are symmetric tri-block copolymers consisting of propylene oxide (PO) and ethylene oxide (EO). The polypropylene oxide block, PPO is sandwiched between two polyethylene oxide (PEO) blocks. The PEO blocks are hydrophilic while PPO is hydrophobic portion in the Pluronic molecule. Due to this structure, we propose that the fatty acid molecules that are in monomeric form most effectively diffuse between the PEO "tails" and bind to the hydrophobic PPO groups.

Mechanisms of chain adsorption on porous substrates and critical conditions of polymer chromatography.

PubMed

Cimino, Richard T; Rasmussen, Christopher J; Brun, Yefim; Neimark, Alexander V

2016-11-01

Polymer adsorption is a ubiquitous phenomenon with numerous technological and healthcare applications. The mechanisms of polymer adsorption on surfaces and in pores are complex owing to a competition between various entropic and enthalpic factors. Due to adsorption of monomers to the surface, the chain gains in enthalpy yet loses in entropy because of confining effects. This competition leads to the existence of critical conditions of adsorption when enthalpy gain and entropy loss are in balance. The critical conditions are controlled by the confining geometry and effective adsorption energy, which depends on the solvent composition and temperature. This phenomenon has important implications in polymer chromatography, since the retention at the critical point of adsorption (CPA) is chain length independent. However, the mechanisms of polymer adsorption in pores are poorly understood and there is an ongoing discussion in the theoretical literature about the very existence of CPA for polymer adsorption on porous substrates. In this work, we examine the mechanisms of chain adsorption on a model porous substrate using Monte Carlo (MC) simulations. We distinguish three adsorption mechanisms depending on the chain location: on external surface, completely confined in pores, and also partially confined in pores in so-called "flower" conformations. The free energies of different conformations of adsorbed chains are calculated by the incremental gauge cell MC method that allows one to determine the partition coefficient as a function of the adsorption potential, pore size, and chain length. We confirm the existence of the CPA for chain length independent separation on porous substrates, which is explained by the dominant contributions of the chain adsorption at the external surface, in particular in flower conformations. Moreover, we show that the critical conditions for porous and nonporous substrates are identical and depend only on the surface chemistry. The theoretical results are confirmed by comparison with experimental data on chromatographic separation of a series of linear polystyrenes. Copyright © 2016 Elsevier Inc. All rights reserved.

Dependence of the product chain-length on detergents for long-chain E-polyprenyl diphosphate synthases

PubMed Central

Pan, Jian-Jung; Ramamoorthy, Gurusankar; Poulter, C. Dale

2013-01-01

Long-chain E-polyprenyl diphosphate synthases (E-PDS) catalyze repetitive addition of isopentenyl diphosphate (IPP) to the growing prenyl chain of an allylic diphosphate. The polyprenyl diphosphate products are required for the biosynthesis of ubiquinones and menaquinones required for electron transport during oxidative phosphorylation to generate ATP. In vitro, the long-chain PDSs require addition of phospholipids or detergents to the assay buffer to enhance product release and maintain efficient turnover. During preliminary assays of product chain-length with anionic, zwitterionic, and non-ionic detergents, we discovered considerable variability. Examination of a series of non-ionic PEG detergents with several long-chain E-PDSs from different organisms revealed that in vitro incubations with nonaethylene glycol monododecyl ether or Triton X-100 typically gave chain lengths that corresponded to those of the isoprenoid moieties in respiratory quinones synthesized in vivo. In contrast incubations in buffer with n-butanol, CHAPS, DMSO, n-octyl-β-glucopyranoside, or β-cyclodextrin or in buffer without detergent typically proceeded more slowly and gave a broad range of chain lengths. PMID:23802587

Tunnel current across linear homocatenated germanium chains

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2014-01-01

The electronic transport properties of germanium oligomers catenating into linear chains (linear Ge chains) have been theoretically studied using first principle methods. The conduction mechanism of a Ge chain sandwiched between gold electrodes was analyzed based on the density of states and the eigenstates of the molecule in a two-probe environment. Like that of silicon chains (Si chains), the highest occupied molecular orbital of Ge chains contains the extended σ-conjugation of Ge 4p orbitals at energy levels close to the Fermi level; this is in contrast to the electronic properties of linear carbon chains. Furthermore, the conductance of a Ge chain is expected to decrease exponentially with molecular length L. The decay constant β, which is defined as e-βL, of a Ge chain is similar to that of a Si chain, whereas the conductance of the Ge chains is higher than that of Si chains even though the Ge-Ge bond length is longer than the Si-Si bond length.

ECERIFERUM2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation.

PubMed

Haslam, Tegan M; Haslam, Richard; Thoraval, Didier; Pascal, Stéphanie; Delude, Camille; Domergue, Frédéric; Fernández, Aurora Mañas; Beaudoin, Frédéric; Napier, Johnathan A; Kunst, Ljerka; Joubès, Jérôme

2015-03-01

The extension of very-long-chain fatty acids (VLCFAs) for the synthesis of specialized apoplastic lipids requires unique biochemical machinery. Condensing enzymes catalyze the first reaction in fatty acid elongation and determine the chain length of fatty acids accepted and produced by the fatty acid elongation complex. Although necessary for the elongation of all VLCFAs, known condensing enzymes cannot efficiently synthesize VLCFAs longer than 28 carbons, despite the prevalence of C28 to C34 acyl lipids in cuticular wax and the pollen coat. The eceriferum2 (cer2) mutant of Arabidopsis (Arabidopsis thaliana) was previously shown to have a specific deficiency in cuticular waxes longer than 28 carbons, and heterologous expression of CER2 in yeast (Saccharomyces cerevisiae) demonstrated that it can modify the acyl chain length produced by a condensing enzyme from 28 to 30 carbon atoms. Here, we report the physiological functions and biochemical specificities of the CER2 homologs CER2-LIKE1 and CER2-LIKE2 by mutant analysis and heterologous expression in yeast. We demonstrate that all three CER2-LIKEs function with the same small subset of condensing enzymes, and that they have different effects on the substrate specificity of the same condensing enzyme. Finally, we show that the changes in acyl chain length caused by each CER2-LIKE protein are of substantial importance for cuticle formation and pollen coat function. © 2015 American Society of Plant Biologists. All Rights Reserved.

ECERIFERUM2-LIKE Proteins Have Unique Biochemical and Physiological Functions in Very-Long-Chain Fatty Acid Elongation1[OPEN

PubMed Central

Haslam, Tegan M.; Haslam, Richard; Thoraval, Didier; Pascal, Stéphanie; Delude, Camille; Domergue, Frédéric; Fernández, Aurora Mañas; Beaudoin, Frédéric; Napier, Johnathan A.; Kunst, Ljerka; Joubès, Jérôme

2015-01-01

The extension of very-long-chain fatty acids (VLCFAs) for the synthesis of specialized apoplastic lipids requires unique biochemical machinery. Condensing enzymes catalyze the first reaction in fatty acid elongation and determine the chain length of fatty acids accepted and produced by the fatty acid elongation complex. Although necessary for the elongation of all VLCFAs, known condensing enzymes cannot efficiently synthesize VLCFAs longer than 28 carbons, despite the prevalence of C28 to C34 acyl lipids in cuticular wax and the pollen coat. The eceriferum2 (cer2) mutant of Arabidopsis (Arabidopsis thaliana) was previously shown to have a specific deficiency in cuticular waxes longer than 28 carbons, and heterologous expression of CER2 in yeast (Saccharomyces cerevisiae) demonstrated that it can modify the acyl chain length produced by a condensing enzyme from 28 to 30 carbon atoms. Here, we report the physiological functions and biochemical specificities of the CER2 homologs CER2-LIKE1 and CER2-LIKE2 by mutant analysis and heterologous expression in yeast. We demonstrate that all three CER2-LIKEs function with the same small subset of condensing enzymes, and that they have different effects on the substrate specificity of the same condensing enzyme. Finally, we show that the changes in acyl chain length caused by each CER2-LIKE protein are of substantial importance for cuticle formation and pollen coat function. PMID:25596184

Role of special cross-links in structure formation of bacterial DNA polymer

NASA Astrophysics Data System (ADS)

Agarwal, Tejal; Manjunath, G. P.; Habib, Farhat; Lakshmi Vaddavalli, Pavana; Chatterji, Apratim

2018-01-01

Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain even of a simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify the large scale structure of a polymer chain with a few cross-links.

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

PubMed Central

Daidone, Isabella; Neuweiler, Hannes; Doose, Sören; Sauer, Markus; Smith, Jeremy C.

2010-01-01

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events. PMID:20098498

Quantum communication beyond the localization length in disordered spin chains.

PubMed

Allcock, Jonathan; Linden, Noah

2009-03-20

We study the effects of localization on quantum state transfer in spin chains. We show how to use quantum error correction and multiple parallel spin chains to send a qubit with high fidelity over arbitrary distances, in particular, distances much greater than the localization length of the chain.

Crossover transition in flowing granular chains

NASA Astrophysics Data System (ADS)

Ulrich, Xialing; Fried, Eliot; Shen, Amy Q.

2009-09-01

We report on the dynamical and statistical behavior of flowing collections of granular chains confined two-dimensionally (2D) within a rotating tumbler. Experiments are conducted with systems of chains of fixed length, but various lengths are considered. The dynamics are punctuated by cascades of chains along a free-surface cascades, which drive the development of mixed porous/laminar packing arrangements in bulk. We investigate the conformation of the system, as characterized by the porosity of the flow region occupied by the chains and the mean-square end-to-end distance of the chains during flow. Both of these measures show crossover transitions from a 2D self-avoiding walk to a 2D random walk when the chain length becomes long enough to allow self-contact.

Majorana bound states in the finite-length chain

NASA Astrophysics Data System (ADS)

Zvyagin, A. A.

2015-08-01

Recent experiments investigating edge states in ferromagnetic atomic chains on superconducting substrate are analyzed. In particular, finite size effects are considered. It is shown how the energy of the Majorana bound state depends on the length of the chain, as well as on the parameters of the model. Oscillations of the energy of the bound edge state in the chain as a function of the length of the chain, and as a function of the applied voltage (or the chemical potential) are studied. In particular, it has been shown that oscillations can exist only for some values of the effective potential.

Nanoparticle stability in semidilute and concentrated polymer solutions.

PubMed

Dutta, Nupur; Green, David

2008-05-20

The wetting of PDMS-grafted silica spheres (PDMS- g-silica) is connected to their depletion restabilization in semidilute and concentrated PDMS/cyohexane polymer solutions. Specifically, we found that a wetting diagram of chemically identical graft and free homopolymers predicts stability of hard, semisoft, and soft spheres as a function of the bulk free polymer volume fraction, graft density, and the graft and free polymer chain lengths. The transition between stable and aggregated regions is determined optically and with dynamic light scattering. The point of demarcation between the regions occurs when the graft and free polymer chains are equal in length. When graft chains are longer than free chains, the particles are stable; in contrast, the particles are unstable when the opposite is true. The regions of particle stability and instability are corroborated with theoretical self-consistent mean-field calculations, which not only show that the grafted brush is responsible for particle dispersion in the complete wetting region but also aggregation in the incomplete wetting region. Ultimately, our results indicate that depletion restabilization depends on the interfacial properties of the nanoparticles in semidilute and concentrated polymer solutions.

Novel guanidine-containing molecular transporters based on lactose scaffolds: lipophilicity effect on the intracellular organellar selectivity.

PubMed

Biswas, Goutam; Jeon, Ock-Youm; Lee, Woo Sirl; Kim, Dong-Chan; Kim, Kyong-Tai; Lee, Suho; Chang, Sunghoe; Chung, Sung-Kee

2008-01-01

We have synthesized two lactose-based molecular transporters, each containing seven guanidine residues attached to the lactose scaffold through omega-aminocarboxylate linker chains of two different lengths, and have examined their cellular uptakes and intracellular and organellar localizations in HeLa cells, as well as their tissue distributions in mice. Both molecular transporters showed higher cellular uptake efficiencies than Arg8, and wide tissue distributions including the brain. Mitochondrial localization is of special interest because of its potential relevance to "mitochondrial diseases". Interestingly, it has been found that the intracellular localization sites of the G7 molecular transporters-namely either mitochondria or lysosomes and endocytic vesicles-are largely determined by the linker chain lengths, or their associated lipophilicities.

Antioxidative effect of lipophilized caffeic acid in fish oil enriched mayonnaise and milk.

PubMed

Alemán, Mercedes; Bou, Ricard; Guardiola, Francesc; Durand, Erwann; Villeneuve, Pierre; Jacobsen, Charlotte; Sørensen, Ann-Dorit Moltke

2015-01-15

The antioxidative effect of lipophilized caffeic acid was assessed in two different fish oil enriched food products: mayonnaise and milk. In both emulsion systems, caffeic acid esterified with fatty alcohols of different chain lengths (C1-C20) were better antioxidants than the original phenolic compound. The optimal chain length with respect to protection against oxidation was, however, different for the two food systems. Fish oil enriched mayonnaise with caffeates of medium alkyl chain length (butyl, octyl and dodecyl) added resulted in a better oxidative stability than caffeates with shorter (methyl) or longer (octadecyl) alkyl chains. Whereas in fish oil enriched milk emulsions the most effective caffeates were those with shorter alkyl chains (methyl and butyl) rather than the ones with medium and long chains (octyl, dodecyl, hexadecyl and eicosyl). These results demonstrate that there might be an optimum alkyl chain length for each phenolipid in each type of emulsion systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

The effect of carbon chain length of starting materials on the formation of carbon dots and their optical properties

NASA Astrophysics Data System (ADS)

Pan, Xiaohua; Zhang, Yan; Sun, Xiaobo; Pan, Wei; Yu, Guifeng; Si, Shuxin; Wang, Jinping

2018-04-01

Carbon dots (CDs) have attracted increasing attention due to their high performances and potential applications in wide range of areas. However, their emission mechanism is not clear so far. In order to reveal more factors contributing to the emission of CDs, the effect of carbon chain length of starting materials on the formation of CDs and their optical properties was experimentally investigated in this work. In order to focus on the effect of carbon chain length, the starting materials with C, O, N in fully identical forms and only carbon chain lengths being different were selected for synthesizing CDs, including citric acid (CA) and adipic acid (AA) as carbon sources, and diamines with different carbon chain lengths (H2N(CH2)nNH2, n = 2, 4, 6) as nitrogen sources, as well as ethylenediamine (EDA) as nitrogen source and diacids with different carbon chain lengths (HOOC(CH2)nCOOH, n = 0, 2, 4, 6) as carbon sources. Therefore, the effect of carbon chain length of starting materials on the formation and optical properties of CDs can be systematically investigated by characterizing and comparing the structures and optical properties of as-prepared nine types of CDs. Moreover, the density of –NH2 on the surface of the CDs was quantitatively detected by a spectrophotometry so as to elucidate the relationship between the –NH2 related surface state and the optical properties.

Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds.

PubMed

Walther, Stefanie; Tietze, Manfred; Czerny, Claus-Peter; König, Sven; Diesterbeck, Ulrike S

2016-01-01

We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11-47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism.

Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds

PubMed Central

Czerny, Claus-Peter; König, Sven; Diesterbeck, Ulrike S.

2016-01-01

We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11–47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism. PMID:27828971

Tracking polypeptide folds on the free energy surface: effects of the chain length and sequence.

PubMed

Brukhno, Andrey V; Ricchiuto, Piero; Auer, Stefan

2012-07-26

Characterization of the folding transition in polypeptides and assessing the thermodynamic stability of their structured folds are of primary importance for approaching the problem of protein folding. We use molecular dynamics simulations for a coarse grained polypeptide model in order to (1) obtain the equilibrium conformation diagram of homopolypeptides in a broad range of the chain lengths, N = 10, ..., 100, and temperatures, T (in a multicanonical ensemble), and (2) determine free energy profiles (FEPs) projected onto an optimal, so-called "natural", reaction coordinate that preserves the height of barriers and the diffusion coefficients on the underlying free energy hyper-surface. We then address the following fundamental questions. (i) How well does a kinetically determined free energy landscape of a single chain represent the polypeptide equilibrium (ensemble) behavior? In particular, under which conditions might the correspondence be lost, and what are the possible implications for the folding processes? (ii) How does the free energy landscape depend on the chain length (homopolypeptides) and the monomer interaction sequence (heteropolypeptides)? Our data reveal that at low T values equilibrium structures adopted by relatively short homopolypeptides (N < 60) are dominated by α-helical folds which correspond to the primary and secondary minima of the FEP. In contrast, longer homopolypeptides (N > 70), upon quasi-equilibrium cooling, fold preferentially in β-bundles with small helical portions, while the FEPs exhibit no distinct global minima. Moreover, subject to the choice of the initial configuration, at sufficiently low T, essentially metastable structures can be found and prevail far from the true thermodynamic equilibrium. We also show that, by sequence-enabling the polypeptide model, it is possible to restrict the chain to a very specific part of the configuration space, which results in substantial simplification and smoothing of the free energy landscape as compared to the case of the corresponding homopolypeptide.

Unit and internal chain profile of African rice (Oryza glaberrima) amylopectin.

PubMed

Gayin, Joseph; Abdel-Aal, El-Sayed M; Manful, John; Bertoft, Eric

2016-02-10

High-performance anion-exchange chromatography was used to study the unit chain profiles of amylopectins and their φ,β-limit dextrins from two African rice (Oryza glaberrima) accessions-TOG 12440 and IRGC 103759. The samples were compared with two Asian rice (Oryza sativa) samples (cv Koshihikari and cv WITA 4) and one O. sativa × O. glaberrima cross (NERICA 4). The ratio of short:long chains ranged between 12.1 and 13.8, and the ratio of A:B-chains was ∼ 1.0 in all samples. A significant difference was observed in the distribution of internal chains with regards to the proportion of short "fingerprint" B-chains (Bfp-chains), which in the φ,β-limit dextrins have a degree of polymerization (DP) 3-7. The African rice starches and NERICA 4 had higher levels of Bfp-chains, but the major group of short B-chains (DP 8-25) was similar to that of the Asian rice samples. The average chain length (CL), internal chain length (ICL), and total internal chain length (TICL) were similar in all samples. However, the external chain length (ECL) was longer in the African rice samples and NERICA 4. ECL correlated positively and significantly (p<0.05) with gelatinization transition temperatures and enthalpy suggesting differences between the two rice types in cooking properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review.

PubMed

Rittman, Martyn; Gilroy, Emma; Koohya, Hashem; Rodger, Alison; Richards, Adair

2009-01-01

Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.

[Construction of dengue virus-specific full-length fully human antibody libraries by mammalian display technology].

PubMed

Wen, Yangming; Lan, Kaijian; Wang, Junjie; Yu, Jingyi; Qu, Yarong; Zhao, Wei; Zhang, Fuchun; Tan, Wanlong; Cao, Hong; Zhou, Chen

2013-06-01

To construct dengue virus-specific full-length fully human antibody libraries using mammalian cell surface display technique. Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) from convalescent patients with dengue fever. The reservoirs of the light chain and heavy chain variable regions (LCκ and VH) of the antibody genes were amplified by RT-PCR and inserted into the vector pDGB-HC-TM separately to construct the light chain and heavy chain libraries. The library DNAs were transfected into CHO cells and the expression of full-length fully human antibodies on the surface of CHO cells was analyzed by flow cytometry. Using 1.2 µg of the total RNA isolated from the PBMCs as the template, the LCκ and VH were amplified and the full-length fully human antibody mammalian display libraries were constructed. The kappa light chain gene library had a size of 1.45×10(4) and the heavy chain gene library had a size of 1.8×10(5). Sequence analysis showed that 8 out of the 10 light chain clones and 7 out of the 10 heavy chain clones randomly picked up from the constructed libraries contained correct open reading frames. FACS analysis demonstrated that all the 15 clones with correct open reading frames expressed full-length antibodies, which could be detected on CHO cell surfaces. After co-transfection of the heavy chain and light chain gene libraries into CHO cells, the expression of full-length antibodies on CHO cell surfaces could be detected by FACS analysis with an expressible diversity of the antibody library reaching 1.46×10(9) [(1.45×10(4)×80%)×(1.8×10(5)×70%)]. Using 1.2 µg of total RNA as template, the LCκ and VH full-length fully human antibody libraries against dengue virus have been successfully constructed with an expressible diversity of 10(9).

Understanding the effect of alkyl chains of gemini cations on the physicochemical and cellular properties of polyurethane micelles.

PubMed

Pan, Zhicheng; Fang, Danxuan; Song, Yuanqing; Song, Nijia; Ding, Mingming; Li, Jiehua; Luo, Feng; Li, Jianshu; Tan, Hong; Fu, Qiang

2018-06-06

Cationic gemini quaternary ammonium (GQA) has been used as a cell internalization promoter to improve the permeability of the cell membrane and enhance the cellular uptake. However, the effect of the alkyl chain length on the cellular properties of nanocarriers has not been elucidated yet. In this study, we developed a series of polyurethane micelles containing GQAs with various alkyl chain lengths. The alteration of the gemini alkyl chain length was found to change the distribution of GQA surfactants in the micellar structure and affect the surface charge exposure, stability, and the protein absorption properties of nanocarriers. Moreover, we also clarified the role of the alkyl chain length in tumor cell internalization and macrophage uptake of polyurethane micelles. This work provides a new understanding on the effect of the GQA alkyl chain length on the physicochemical and biological properties of nanomedicines, and offers guidance on the rational design of effective drug delivery systems where the issue of functional group exposure at the micellar surface should be considered.

Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

PubMed

Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

2011-07-21

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

Structure of gel phase saturated lecithin bilayers: temperature and chain length dependence.

PubMed Central

Sun, W J; Tristram-Nagle, S; Suter, R M; Nagle, J F

1996-01-01

Systematic low-angle and wide-angle x-ray scattering studies have been performed on fully hydrated unoriented multilamamellar vesicles of saturated lecithins with even chain lengths N = 16, 18, 20, 22, and 24 as a function of temperature T in the normal gel (L beta') phase. For all N, the area per chain Ac increases linearly with T with an average slope dAc/dT = 0.027 A2/degree C, and the lamellar D-spacings also increase linearly with an average slope dD/dT = 0.040 A/degree C. At the same T, longer chain length lecithins have more densely packed chains, i.e., smaller Ac's, than shorter chain lengths. The chain packing of longer chain lengths is found to be more distorted from hexagonal packing than that of smaller N, and the distortion epsilon of all N approaches the same value at the respective transition temperatures. The thermal volume expansion of these lipids is accounted for by the expansion in the hydrocarbon chain region. Electron density profiles are constructed using four orders of low-angle lamellar peaks. These show that most of the increase in D with increasing T is due to thickening of the bilayers that is consistent with a decrease in tilt angle theta and with little change in water spacing with either T or N. Because of the opposing effects of temperature on area per chain Ac and tilt angle 0, the area expansivity alpha A is quite small. A qualitative theoretical model based on competing head and chain interactions accounts for our results. PMID:8842227

Studies on long chain cis- and trans-acyl-CoA esters and Acyl-CoA dehydrogenase from rat heart mitochondria.

PubMed

Korsrud, G O; Conacher, H B; Jarvis, G A; Beare-Rogers, J L

1977-02-01

The beta-oxidation of long chain fatty acids was investigated in a preparation of rat heart mitochondria. The acyl-CoA esters of the cis and trans isomers of delta9-hexadecenoic, delta9-octadecenoic, delta11-eicosenoic, and delta13-docosenoic acids were prepared. Rates of the acyl-CoA reaction were determined with an extract from rat heart mitochondria. The apparent Michaelis constant (Km) and maximum velocity (Vmax) were calculated for each substrate. In general, apparent Vmax values decreased with increasing chain length of the monoenoic substrates. Reduced activity of acyl-CoA dehydrogenase with long chain acyl-CoA esters could have contributed to accumulation of lipids in hearts of rats fed diets containing long chain fatty acids.

Biosynthesis of medium chain length alkanes for bio-aviation fuel by metabolic engineered Escherichia coli.

PubMed

Wang, Meng; Nie, Kaili; Cao, Hao; Xu, Haijun; Fang, Yunming; Tan, Tianwei; Baeyens, Jan; Liu, Luo

2017-09-01

The aim of this work was to study the synthesis of medium-chain length alkanes (MCLA), as bio-aviation product. To control the chain length of alkanes and increase the production of MCLA, Escherichia coli cells were engineered by incorporating (i) a chain length specific thioesterase from Umbellularia californica (UC), (ii) a plant origin acyl carrier protein (ACP) gene and (iii) the whole fatty acid synthesis system (FASs) from Jatropha curcas (JC). The genetic combination was designed to control the product spectrum towards optimum MCLA. Decanoic, lauric and myristic acid were produced at concentrations of 0.011, 0.093 and 1.657mg/g, respectively. The concentration of final products nonane, undecane and tridecane were 0.00062mg/g, 0.0052mg/g, and 0.249mg/g respectively. Thioesterase from UC controlled the fatty acid chain length in a range of 10-14 carbons and the ACP gene with whole FASs from JC significantly increased the production of MCLA. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of amylose nanoparticles prepared via nanoprecipitation: Influence of chain length distribution.

PubMed

Chang, Yanjiao; Yang, Jingde; Ren, Lili; Zhou, Jiang

2018-08-15

The influence of chain length distribution of amylose on size and structure of the amylose nanoparticles (ANPs) prepared through nanoprecipitation was investigated. Amylose with different chain length distributions was obtained by β-amylase treating amylose paste for different times and measured by size exclusion chromatography (SEC) and fluorophore-assisted carbohydrate electrophoresis (FACE). ANPs prepared via precipitation were characterized by using dynamic light scattering (DLS), scanning electron microscopy (SEM) and X-ray diffraction (XRD). Results showed that the β-amylase treatments led to decrease in chain length of amylose, and it was the most important factor affecting size of ANPs. When hydrolysis degree of amylose was 52.8%, mean size of ANPs decreased from 206.4 nm to 102.7 nm. All the ANPs displayed a V-type crystalline structure and the effect of amylose chain length on crystallinity of the precipitated ANPs was negligible in the investigated range. Copyright © 2018 Elsevier Ltd. All rights reserved.

Exploring the impact of the side-chain length on peptide/RNA binding events.

PubMed

Sbicca, Lola; González, Alejandro López; Gresika, Alexandra; Di Giorgio, Audrey; Closa, Jordi Teixido; Tejedor, Roger Estrada; Andréola, Marie-Line; Azoulay, Stéphane; Patino, Nadia

2017-07-19

The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (K D ) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.

Reversed-phase high-performance liquid chromatography purification of methyl esters of C(16)-C(28) polyunsaturated fatty acids in microalgae, including octacosaoctaenoic acid [28:8(n-3)].

PubMed

Mansour, Maged P

2005-12-02

A preparative reversed-phase (RP; C(18)) high-performance liquid chromatography (HPLC) method with gradient elution using acetonitrile (MeCN)-chloroform (CHCl(3)) (or dichloromethane (DCM)) and evaporative light-scattering detection (ELSD) with automatic multiple injection and fraction collection was used to purify milligram quantities of microalgal polyunsaturated fatty acids (PUFA), separated as methyl esters (ME). PUFA-ME purified included methyl esters of docosahexaenoic acid (DHA; 22:6(n-3)), eicosapentaenoic acid (EPA; 20:5(n-3)) and the unusual very long-chain (C(28)) highly unsaturated fatty acid (VLC-HUFA), octacosaoctaenoic acid [28:8(n-3)(4, 7, 10, 13, 16, 19, 22, 25)] from the marine dinoflagellate Scrippsiella sp. CS-295/c. Other PUFA purified from various microalgae using this RP-HPLC method to greater than 95% purity included 16:3(n-4), 16:4(n-3), 16:4(n-1) and 18:5(n-3). The number of injections required was variable and depended on the abundance of the desired PUFA-ME, and resolution from closely eluting PUFA-ME, which determined the maximum loading. The purity of these fatty acids was determined by electron impact (EI) GC-MS and the chain length and location of double bonds was determined by EI GC-MS of 4,4-dimethyl oxazoline (DMOX) derivatives formed using a low temperature method. Advantages over silver-ion HPLC for purifying PUFA-ME is that separation occurs according to chain length as well as degree of unsaturation enabling separation of PUFA-ME with the same degree of unsaturation but different chain length (i.e. between 18:5(n-3) and 20:5(n-3)). In addition, PUFA-ME are not strongly adsorbed, but elute earlier than their more saturated corresponding FAME of the same chain length. This method is robust, simple, and requires only a short re-equilibration time. It is a useful tool for preparing milligram quantities of pure PUFA-ME for bioactive screening (as free fatty acids), although many multiple injections may be required for minor PUFA-ME. It also enabled dose-response and structure-activity studies to be carried out. It can be used for the enrichment of low levels of VLC-HUFA-ME to facilitate elucidation of their chemical structure and so is a useful adjunct to EI GC-MS of DMOX derivatives and other techniques such as NMR, which requires milligram quantities of purified compounds.

Flexible chain molecules in the marginal and concentrated regimes: universal static scaling laws and cross-over predictions.

PubMed

Laso, Manuel; Karayiannis, Nikos Ch

2008-05-07

We present predictions for the static scaling exponents and for the cross-over polymer volumetric fractions in the marginal and concentrated solution regimes. Corrections for finite chain length are made. Predictions are based on an analysis of correlated fluctuations in density and chain length, in a semigrand ensemble in which mers and solvent sites exchange identities. Cross-over volumetric fractions are found to be chain length independent to first order, although reciprocal-N corrections are also estimated. Predicted scaling exponents and cross-over regimes are compared with available data from extensive off-lattice Monte Carlo simulations [Karayiannis and Laso, Phys. Rev. Lett. 100, 050602 (2008)] on freely jointed, hard-sphere chains of average lengths from N=12-500 and at packing densities from dilute ones up to the maximally random jammed state.

n-Alkane adsorption to polar silica surfaces.

PubMed

Brindza, Michael R; Ding, Feng; Fourkas, John T; Walker, Robert A

2010-03-21

The structures of medium-length n-alkane species (C(8)-C(11)) adsorbed to a hydrophilic silica/vapor interface were examined using vibrational sum frequency spectroscopy. Experiments sampling out-of-plane orientation show a clear pattern in vibrational band intensities that implies chains having primarily all-trans conformations lying flat along the interface. Further analysis shows that the methylene groups of the alkane chains have their local symmetry axes directed into and away from the surface. Spectra acquired under different polarization conditions interlock to reinforce this picture of interfacial structure and organization. Variation in signal intensities with chain length suggests that correlation between adsorbed monomers weakens with increasing chain length. This result stands in contrast with alkane behavior at neat liquid/vapor interfaces where longer length alkanes show considerably more surface induced ordering than short chain alkanes.

Excess entropy scaling for the segmental and global dynamics of polyethylene melts.

PubMed

Voyiatzis, Evangelos; Müller-Plathe, Florian; Böhm, Michael C

2014-11-28

The range of validity of the Rosenfeld and Dzugutov excess entropy scaling laws is analyzed for unentangled linear polyethylene chains. We consider two segmental dynamical quantities, i.e. the bond and the torsional relaxation times, and two global ones, i.e. the chain diffusion coefficient and the viscosity. The excess entropy is approximated by either a series expansion of the entropy in terms of the pair correlation function or by an equation of state for polymers developed in the context of the self associating fluid theory. For the whole range of temperatures and chain lengths considered, the two estimates of the excess entropy are linearly correlated. The scaled bond and torsional relaxation times fall into a master curve irrespective of the chain length and the employed scaling scheme. Both quantities depend non-linearly on the excess entropy. For a fixed chain length, the reduced diffusion coefficient and viscosity scale linearly with the excess entropy. An empirical reduction to a chain length-independent master curve is accessible for both dynamic quantities. The Dzugutov scheme predicts an increased value of the scaled diffusion coefficient with increasing chain length which contrasts physical expectations. The origin of this trend can be traced back to the density dependence of the scaling factors. This finding has not been observed previously for Lennard-Jones chain systems (Macromolecules, 2013, 46, 8710-8723). Thus, it limits the applicability of the Dzugutov approach to polymers. In connection with diffusion coefficients and viscosities, the Rosenfeld scaling law appears to be of higher quality than the Dzugutov approach. An empirical excess entropy scaling is also proposed which leads to a chain length-independent correlation. It is expected to be valid for polymers in the Rouse regime.

FACTORS AFFECTING THE CHAIN LENGTH OF GROUP A STREPTOCOCCI

PubMed Central

Ekstedt, Richard D.; Stollerman, Gene H.

1960-01-01

Group A streptococci which grew in long chains in the presence of homologous anti-M antibody were split into their original length by the addition of an excess of homologous M protein to the culture. The chain-splitting reaction showed temperature and pH optima (37°C., 7.5) and was completely inhibited at 0°C. or by heat-killing the long chains at 56°C. prior to the addition of M protein. Addition of sublethal doses of HgCl2, or of penicillin, inhibited the chain-splitting reaction. Pneumococci behaved in entirely comparable fashion to streptococci in similar experiments. Virulent strains of streptococci formed the shortest chains when broth media was enriched with serum. The chain-shortening effect of serum enrichment of the media was most apparent with encapsulated strains and under cultural conditions that favored capsule formation. Loss of capsules by mutation or by unfavorable growth conditions resulted in increase in chain length. The activity of the chain-splitting mechanism seemed to be independent of M protein, however, since encapsulated M-negative variants also formed very short chain in serum-enriched media. The physical presence of the capsule was not essential for chain shortening since enzymatic removal of the capsule with hyaluronidase during growth did not affect chain length. These results strongly suggest that chain-splitting of streptococci and pneumococci occurs by an active metabolic mechanism, presumably enzymatic, which is inhibited by the union of surface antigens with specific antibody. PMID:13726267

Synthesis and Solution Properties of Adamantane Containing Quaternary Ammonium Salt-type Cationic Surfactants: Hydrocarbon-based, Fluorocarbonbased and Bola-type.

PubMed

Yoshimura, Tomokazu; Okada, Mari; Matsuoka, Keisuke

2016-10-01

Quaternary ammonium salt-type cationic surfactants with an adamantyl group (hydrocarbon-type; C n AdAB, fluorocarbon-type; C m F C 3 AdAB, bola-type; Ad-s-Ad, where n, m and s represent hydrocarbon chain lengths of 8-16, fluorocarbon chain lengths of 4-8, and spacer chain length of 10-12) were synthesized via quaternization of N, N-dimethylaminoadamantane and n-alkyl bromide or 1, n-dibromoalkane. Conductivity and surface tension were measured to characterize the solution properties of the synthesized adamantyl group-containing cationic surfactants. In addition, the effects of hydrocarbon and fluorocarbon chain lengths and spacer chain length between headgroups on the measured properties were evaluated by comparison with those of conventional cationic surfactants. The critical micelle concentration (CMC) of C n AdAB and Ad-s-Ad was 2/5 of that for the corresponding conventional surfactants C n TAB and bola-type surfactants with similar number of carbons in the alkyl or alkylene chain; this was because of the increased hydrophobicity due to the adamantyl group. A linear relationship between the logarithm of CMC and the hydrocarbon chain length for C n AdAB was observed, as well as for C n TAB. The slope of the linear correlation for both surfactants was almost the same, indicating that the adamantyl group does not affect the CMC with variations in the hydrocarbon chain length. Similar to conventional surfactants C n TAB, the hydrocarbon-type C n AdAB is highly efficient in reducing the surface tension of water, despite the large occupied area per molecule resulting from the relatively bulky structure of the adamantane skeleton. On the other hand, the bola-type Ad-s-Ad resulted in increased surface tension compared to C n AdAB, indicating that the curved chain between adamantyl groups leads to poor adsorption and orientation at the air-water interface.

Early Hits and Long-Term Consequences: Tracking the Lasting Impact of Prenatal Smoke Exposure on Telomere Length in Children

PubMed Central

McKasson, Sarah; Mabile, Emily; Dunaway, Lauren F.; Drury, Stacy S.

2013-01-01

We examined the association between telomere length and prenatal tobacco exposure (PTE) in 104 children aged 4 to 14 years. Salivary telomere length (STL) was determined from salivary DNA using quantitative polymerase chain reaction. Of the children, 18% had maternal reported PTE. Mean STL was significantly lower among children with PTE (6.4 vs 7.5, P < .05). Findings extend the literature demonstrating the negative long-term effects of PTE to include a cellular marker of aging linked to multiple negative health outcomes. PMID:23927510

Study on the photo-induced oxygen reordering in YBa2Cu3O6+x

NASA Astrophysics Data System (ADS)

Milić, M. M.; Lazarov, N. Dj.; Cucić, D. A.

2012-05-01

Effect of the long term illumination of the YBa2Cu3O6+x with visible light or ultraviolet irradiation on its superconducting properties was studied in the frame of a simple theoretical model, which assumes that photodoping triggers rearrangement of oxygen monomers in the chain layers thus causing the enhancement of the average chain length, lav. Since, according to the model of charge transfer mechanism, long CuO chains are better electronic hole donors than the short ones, increase of the average chain length induces additional holes transfer from chain layers to the superconducting CuO2 planes which in turn leads to the increase of the superconducting transition temperature Tc. By the use of the expression for the chain length probability distribution and numerically calculated values for the average chain length in the non-excited system, we were able to estimate the doping p (number of holes per one Cu atom in the superconducting CuO2 planes) and Tc enhancement due to photo-induced oxygen reordering. The theoretical results are compared with available experimental data.

The Ultra-filtration of Macromolecules with Different Conformations and Configurations through Nanopores

NASA Astrophysics Data System (ADS)

Ge, Hui

This Ph. D. thesis presents our study on the ultrafiltration of polymers with different configurations and conformations; namly, theoretically, the passing of polymer chains through a nanopore under an elongational flow filed has been studied for years, but experimental studies are rare because of two following reasons: (1) lacks a precise method to investigate how individual single polymer chain pass through a nanopore; (2) it is difficult, if not impossible, to obtain a set of polymer samples with a narrow molar mass distribution and a uniform structures; except for linear chains. The central question in this study is to find the critical (minimum) flow rate (qc) for each kind of chains, at which the chains can pass through a given nanopore. A comparison of the measured and calculated qc leads to a better understanding how different chains are deformed, stretched and pulled through a nanopore. We have developed a novel method of combinating static and dynamic laser light scattering (LLS) to precisely measure the relative retention concentration ((C0 - C)/C0). Chapter 1 briefly introduces the theoretical background of how applications and lists some of resent research progresses in this area. Polymer with various configurations and conformations pass through nanopores; including polymer linear chains, stars polymer, branched polymers, polymer micelles are introduced. Among them, the de Gennes and Brochard-Wyart's predictions of polymer linear and star chains passing through nanopores are emphasized, in which they predicted that qc of linear chain is qc ≃ kBT/(3pieta), where kB, T and eta are the Boltzmann constant, the absolutely temperature, and the viscosity of solvent, respectively, independent of both the chain length and the pore size; and for star chains passing through nanopores, there exist a optimal entering arm numbers, namely, the star chains passing through nanopores. Chapter 2 details basic theory of static and dynamic laser light scattering (LLS), including its instrumentation and our ultrafiltration setup. Chapter 3 briefly introduces the sample preparation, including the history and mechanism of anionic living polymerization, as well as how we used a novel home-made set-up to prepare linear polystyrene with different chain lengths and star polystyrene with various arm numbers and lengths. Chapter 4 summarizes our measured critical flow rates (qc) of linear polymer chains with different lengths for nanopores with different sizes, since the flow rate is directly related to the hydrodynamic force, we have developed a sensitive method (down to tens fN) to directly assess how much the hydrodynamic force (Fh) is required to overcome the weak entropy elasticity and stretch individual coiled chains in solution. Our method is completely different from the using existing optical tweezers or AFM, because they measure the relatively stronger enthalpy elasticity. Our results confirm that qc is indeed independent of the chain length, but decreases as the pore size increases. The value of qc is ˜10--200 times smaller than kBT/(3pieta). Such a discrepancy has been attributed to the rough assumption made by de Gennes and his coworkers; namely, each chain segment "blob" confined inside the pore is not a hard sphere so that the effective length along the flow direction is much longer than the pore diameter. Finally, using the solution temperature, we varied the chain conformation, our result shows that q c has a minimum which is near, but not exactly located at the theta temperature, might leading to a better way to determine the true ideal state of a polymer solution, at which all viral coefficients, not only the second vanish. Chapter 5 uses polymer solutions made of different mixtures of linear and star chains, we have demonstrated that flushing these solution mixtures through a nanopore with a properly chosen flow rate can effectively and cleanly separate linear and star chains no matter whether linear chains are larger or smaller than star chains. Chapter 6 further investigates how star-like polystyrene pass through a given nanopore under the flow field. Star polystyrene chains with different arm lengths (LA) and numbers (f) passing through a nanopore (20 nm) under an elongational flow field was investigated in terms of the flow-rate dependent relative retention ((C0 - C)/C0), where C 0 and C are the polymer concentrations before and after the ultrafiltration. Our results reveal that for a given arm length (LA), the critical flow rate (qc,star), below which star chains are blocked, dramatically increases with the total arm numbers (f); but for a given f, is nearly independent on LA, contradictory to the previous prediction made by de Gennes and Brochard-Wyart. We have revised their theory in the region fin < fout and also accounted for the effective length of each blob, where fin and fout are the numbers of arms inside and outside the pore, respectively. In the revision, we show that qc,star is indeed independent of LA but related to f and f in in two different ways, depending on whether fin ≤ f/2 or ≥ f/2. A comparison of our experimental and calculated results reveals that most of star chains pass through the nanopores with fin ˜ f/2. Further study of the temperature dependent (C0 - C)/C 0 of polystyrene in cyclohexane reveals that there exists a minimum of qc,star at ˜38 °C, close to its theta temperature (-34.5 °C).

Smaller predator-prey body size ratios in longer food chains.

PubMed Central

Jennings, Simon; Warr, Karema J

2003-01-01

Maximum food-chain length has been correlated with resource availability, ecosystem size, environmental stability and colonization history. Some of these correlations may result from environmental effects on predator-prey body size ratios. We investigate relationships between maximum food-chain length, predator-prey mass ratios, primary production and environmental stability in marine food webs with a natural history of community assembly. Our analyses provide empirical evidence that smaller mean predator-prey body size ratios are characteristic of more stable environments and that food chains are longer when mean predator-prey body size ratios are small. We conclude that environmental effects on predator-prey body size ratios contribute to observed differences in maximum food-chain length. PMID:12965034

Novel odd/even effect of alkylene chain length on the photopolymerizability of organogelators.

PubMed

Aoki, Ken'ichi; Kudo, Masabumi; Tamaoki, Nobuyuki

2004-10-28

[reaction: see text] Starting from diactylene diacarboxylic acids, we have synthesized a series of photopolymerizable organogelators that possess simple amide structures, different alkylene chain lengths, and either optically active or racemic 3,7-dimethyl-1-octylamine units. The alkylene chain length of these compounds exhibits a prominent odd/even effect with respect to the photopolymerization in the gel state and is accompanied by a stereostructural effect on the gelation ability.

Thermoreversible gelation of poly(vinylidene fluoride) in phthalates: the influence of aliphatic chain length of solvents.

PubMed

Yadav, P Jaya Prakash; Ghosh, Goutam; Maiti, Biswajit; Aswal, Vinod K; Goyal, P S; Maiti, Pralay

2008-04-17

Thermoreversible gelation of poly(vinylidene fluoride) (PVDF) has been studied in a new series of solvents (phthalates), for example, dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DBP), and dihexyl phthalate (DHP) as a function of temperature and polymer concentration, both by test tube tilting and dynamic light scattering (DLS) method. The effect of aliphatic chain length (n) of diesters on the gelation kinetics, structure/microstructure and morphology of PVDF gels has been examined. Gelation rate was found to increase with increasing aliphatic chain length of diester. DLS results indicate that the sol-gel transformation proceeds via two-steps: first, microgel domains were formed, and then the infinite three-dimensional (3D) network is established by connecting microgels through polymer chains. The crystallites are responsible for 3D network for gelation in phthalates, and alpha-polymorph is formed during gelation producing higher amount of crystallinity with increasing aliphatic chain length of diester. Morphology of the networks of dried gels in different phthalates showed that fibril thickness and lateral dimensions decrease with higher homologues of phthalates. The scattering intensity is fitted with Debye-Bueche model in small-angle neutron scattering and suggested that both the correlation length and interlamellar spacing increases with n. A model has been proposed, based on electronic structure calculations, to explain the conformation of PVDF chain in presence of various phthalates and their complexes, which offer the cause of higher gelation rate for longer aliphatic chain length.

Chain Ends and the Ultimate Tensile Strength of Polyethylene Fibers

NASA Astrophysics Data System (ADS)

O'Connor, Thomas C.; Robbins, Mark O.

Determining the tensile yield mechanisms of oriented polymer fibers remains a challenging problem in polymer mechanics. By maximizing the alignment and crystallinity of polyethylene (PE) fibers, tensile strengths σ ~ 6 - 7 GPa have been achieved. While impressive, first-principal calculations predict carbon backbone bonds would allow strengths four times higher (σ ~ 20 GPa) before breaking. The reduction in strength is caused by crystal defects like chain ends, which allow fibers to yield by chain slip in addition to bond breaking. We use large scale molecular dynamics (MD) simulations to determine the tensile yield mechanism of orthorhombic PE crystals with finite chains spanning 102 -104 carbons in length. The yield stress σy saturates for long chains at ~ 6 . 3 GPa, agreeing well with experiments. Chains do not break but always yield by slip, after nucleation of 1D dislocations at chain ends. Dislocations are accurately described by a Frenkel-Kontorova model, parametrized by the mechanical properties of an ideal crystal. We compute a dislocation core size ξ = 25 . 24 Å and determine the high and low strain rate limits of σy. Our results suggest characterizing such 1D dislocations is an efficient method for predicting fiber strength. This research was performed within the Center for Materials in Extreme Dynamic Environments (CMEDE) under the Hopkins Extreme Materials Institute at Johns Hopkins University. Financial support was provided by Grant W911NF-12-2-0022.

The integrable quantum group invariant A2n-1(2) and Dn+1(2) open spin chains

NASA Astrophysics Data System (ADS)

Nepomechie, Rafael I.; Pimenta, Rodrigo A.; Retore, Ana L.

2017-11-01

A family of A2n(2) integrable open spin chains with Uq (Cn) symmetry was recently identified in arxiv:arXiv:1702.01482. We identify here in a similar way a family of A2n-1(2) integrable open spin chains with Uq (Dn) symmetry, and two families of Dn+1(2) integrable open spin chains with Uq (Bn) symmetry. We discuss the consequences of these symmetries for the degeneracies and multiplicities of the spectrum. We propose Bethe ansatz solutions for two of these models, whose completeness we check numerically for small values of n and chain length N. We find formulas for the Dynkin labels in terms of the numbers of Bethe roots of each type, which are useful for determining the corresponding degeneracies. In an appendix, we briefly consider Dn+1(2) chains with other integrable boundary conditions, which do not have quantum group symmetry.

Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

USDA-ARS?s Scientific Manuscript database

Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic proc...

The Ultrasensitivity of Living Polymers

NASA Astrophysics Data System (ADS)

O'Shaughnessy, Ben; Vavylonis, Dimitrios

2003-03-01

Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: Even a small perturbation (e.g., temperature jump) nonlinearly distorts the CLD, eliminating or massively augmenting short chains. The origin is fast relaxation of mass variables (mean chain length, monomer concentration) which perturbs CLD shape variables before these can relax via slow chain growth rate fluctuations. Viscosity relaxation predictions agree with experiments on the best-studied synthetic system, α-methylstyrene.

Analysis of Nuclear Factor-κB (NF-κB) Essential Modulator (NEMO) Binding to Linear and Lysine-linked Ubiquitin Chains and Its Role in the Activation of NF-κB*

PubMed Central

Kensche, Tobias; Tokunaga, Fuminori; Ikeda, Fumiyo; Goto, Eiji; Iwai, Kazuhiro; Dikic, Ivan

2012-01-01

Nuclear factor-κB (NF-κB) essential modulator (NEMO), a component of the inhibitor of κB kinase (IKK) complex, controls NF-κB signaling by binding to ubiquitin chains. Structural studies of NEMO provided a rationale for the specific binding between the UBAN (ubiquitin binding in ABIN and NEMO) domain of NEMO and linear (Met-1-linked) di-ubiquitin chains. Full-length NEMO can also interact with Lys-11-, Lys-48-, and Lys-63-linked ubiquitin chains of varying length in cells. Here, we show that purified full-length NEMO binds preferentially to linear ubiquitin chains in competition with lysine-linked ubiquitin chains of defined length, including long Lys-63-linked deca-ubiquitins. Linear di-ubiquitins were sufficient to activate both the IKK complex in vitro and to trigger maximal NF-κB activation in cells. In TNFα-stimulated cells, NEMO chimeras engineered to bind exclusively to Lys-63-linked ubiquitin chains mediated partial NF-κB activation compared with cells expressing NEMO that binds to linear ubiquitin chains. We propose that NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. This phenomenon could explain quantitatively distinct NF-κB activation patterns in response to numerous cell stimuli. PMID:22605335

Overlaps with arbitrary two-site states in the XXZ spin chain

NASA Astrophysics Data System (ADS)

Pozsgay, B.

2018-05-01

We present a conjectured exact formula for overlaps between the Bethe states of the spin-1/2 XXZ chain and generic two-site states. The result takes the same form as in the previously known cases: it involves the same ratio of two Gaudin-like determinants, and a product of single-particle overlap functions, which can be fixed using a combination of the quench action and quantum transfer matrix methods. Our conjecture is confirmed by numerical data from exact diagonalization. For one-site states, the formula is found to be correct even in chains with odd length. It is also pointed out that the ratio of the Gaudin-like determinants plays a crucial role in the overlap sum rule: it guarantees that in the thermodynamic limit there remains no term in the quench action.

Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

PubMed Central

Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

2014-01-01

Increasingly, stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ15N, and carbon range (CR) using δ13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ15N or δ13C from source to consumer) between trophic levels and among food chains. δ15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of ecological systems. PMID:24676331

Room temperature structures and odd even behaviour of a homologous series of anhydrous lithium n-alkanoates

NASA Astrophysics Data System (ADS)

White, Nicole A. S.; Ellis, Henry A.

2008-10-01

The molecular structures of a homologous series of lithium n-alkanoates have been determined at room temperature using infrared spectroscopy, polarizing light microscopy and X-ray powder diffraction in conjunction with density and melting point measurements. For all the compounds investigated, asymmetric ionic metal-carboxylate coordination is proposed, with the molecules located within a triclinic crystal system with P1¯ space group. The molecules are nearly all of similar structure and are arranged within lamellar layers with four molecules per unit cell. The hydrocarbon chains, in nearly all trans conformation, are arranged tail-to-tail and tilted at an average angle of 55 ο to the planes containing lithium ions. The unit cell parameters such as sides: b and c increase linearly with increasing chain length whilst side a shows a linear decrease. Furthermore, the measured densities and melting points show odd-even behaviour, suggesting differences in molecular packing between odd and even chain length homologues. Geometric models are proposed to explain molecular orientation within a lamella and odd-even behaviour, involving the influence of terminal groups on the packing geometry of hydrocarbon chains within the lattice.

Globular, Sponge-like to Layer-like Morphological Transition in 1-n-Alkyl-3-methylimidazolium Octylsulfate Ionic Liquid Homologous Series.

PubMed

Kapoor, Utkarsh; Shah, Jindal K

2018-01-11

Segregation of polar and nonpolar domains in ionic liquids for which either the cation or anion is responsible for inducing nonpolar domains is well understood. On the other hand, information regarding the nanoscale heterogeneities originating due to the presence of nonpolar content on both the ions is rudimentary at this point. The present contribution is aimed at addressing this question and focuses on a molecular dynamics simulation study to probe nanoscale structural and aggregation features of the 1-n-alkyl-3-methylimidazolium [C n mim] octylsulfate [C 8 SO 4 ] ionic liquid homologous series (n = 2, 4, 6, 8, 10, and 12). The objective of this work is to determine the effect of increasing alkyl chain length in the cation on nonpolar domain formation, especially when the alkyl chain lengths from both the ions participate in defining such domains. The results indicate that all the ionic liquids form nonpolar domains, morphology of which gradually changes from globular, sponge-like to layer-like structure with increase in the cationic alkyl chain length. The length of the nonpolar domains calculated from the total structure factor for [C 10 mim][C 8 SO 4 ] is considerably higher than that reported for other imidazolium-based ionic liquid containing smaller anions. The structure factor for [C 12 mim][C 8 SO 4 ] ionic liquid contains multiple intermediate peaks separating the charge alternation peak and pre-peak, which points to nonpolar domains of varying lengths, an observation that remains to be validated. Analysis of the heterogeneous order parameters and orientational correlation functions of the alkyl chains further suggests an increase in the spatial heterogeneity and long-range order along the homologous series. The origin of rich diversity of structures obtained by introducing nonpolar content on both the ions is discussed.

Identification of amino acids conferring chain length substrate specificities on fatty alcohol-forming reductases FAR5 and FAR8 from Arabidopsis thaliana.

PubMed

Chacón, Micaëla G; Fournier, Ashley E; Tran, Frances; Dittrich-Domergue, Franziska; Pulsifer, Ian P; Domergue, Frédéric; Rowland, Owen

2013-10-18

Fatty alcohols play a variety of biological roles in all kingdoms of life. Fatty acyl reductase (FAR) enzymes catalyze the reduction of fatty acyl-coenzyme A (CoA) or fatty acyl-acyl carrier protein substrates to primary fatty alcohols. FAR enzymes have distinct substrate specificities with regard to chain length and degree of saturation. FAR5 (At3g44550) and FAR8 (At3g44560) from Arabidopsis thaliana are 85% identical at the amino acid level and are of equal length, but they possess distinct specificities for 18:0 or 16:0 acyl chain length, respectively. We used Saccharomyces cerevisiae as a heterologous expression system to assess FAR substrate specificity determinants. We identified individual amino acids that affect protein levels or 16:0-CoA versus 18:0-CoA specificity by expressing in yeast FAR5 and FAR8 domain-swap chimeras and site-specific mutants. We found that a threonine at position 347 and a serine at position 363 were important for high FAR5 and FAR8 protein accumulation in yeast and thus are likely important for protein folding and stability. Amino acids at positions 355 and 377 were important for dictating 16:0-CoA versus 18:0-CoA chain length specificity. Simultaneously converting alanine 355 and valine 377 of FAR5 to the corresponding FAR8 residues, leucine and methionine, respectively, almost fully converted FAR5 specificity from 18:0-CoA to 16:0-CoA. The reciprocal amino acid conversions, L355A and M377V, made in the active FAR8-S363P mutant background converted its specificity from 16:0-CoA to 18:0-CoA. This study is an important advancement in the engineering of highly active FAR proteins with desired specificities for the production of fatty alcohols with industrial value.

Branching, Chain Scission, and Solution Stability of Worm-Like Micelles

NASA Astrophysics Data System (ADS)

Beaucage, Greg; Vogtt, Karsten; Jiang, Hanqui

As salt is added to a simple micelle solution such as SDS or SLES, the zero shear rate specific viscosity rises rapidly followed by a maximum and decay. The rapid rise in viscosity is associated with formation of elliptical and extended chain worm-like micelles, WLMs. Entanglement of these long chain micelles leads to the viscoelastic behavior we associate with shampoo and body wash. The plateau and drop in viscosity at high salt concentrations is caused by a special type of topological branching where the branch points have no energy penalty to motion along the chain according to Cates theory. These have some similarity to catenane crosslinks. Predictive dynamic theories for WLMs rely on structural details; the diameter, persistence length, contour length, branch length, segment length between branch points, and mesh size. Further, since the contour length and other large scale features are in kinetic equilibrium, with frequent chain breakage and formation, the thermodynamics of these long chain structures are of interest both in terms of chain scission as well as in terms of the stability of the colloidal solution as a whole. Recent structural studies of WLMs using static neutron scattering based on new scattering models will be presented demonstrating that these input parameters for dynamic models of complex topological systems are quantitatively and directly available. In this context it is important to consider a comparison between dynamic features, for instance entanglement, and their static analogs, chain overlap.

Synthesis and characterisation of new types of side chain cholesteryl polymers.

PubMed

Wang, Bin; Du, Haiyan; Zhang, Junhua

2011-01-01

A series of cholesterol derivatives have been synthesised via the alkylation reaction of the 3-hydroxyl group with the aliphatic bromide compounds with different chain lengths, namely 3β-alkyloxy-cholesterol. The double bond between the C5 and C6 positions in these cholesterol derivatives was oxidised into epoxy, followed by an epoxy-ring-opening reaction with the treatment with acrylic acid, resulting in a series of 3β-alkyloxy-5α-hydroxy-6β-acryloyloxycholesterol, C(n)OCh (n=1, 2, 4, 6, 8, 10, 12), The acrylate group is connected to the C6 position, which is confirmed by the single crystal structure analysis. The corresponding polymers, PC(n)OCh, were prepared via free radical polymerisation. The structure of monomers and the resulting polymers were characterised with nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). The thermal properties of PC(n)OCh were studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To determine the secondary structure of polymers, circular dichroism (CD) spectra were performed. It was found that not all monomers produce high-molecular-weight polymers because of steric hindrance. However, all polymers have a helical structure, which can be enhanced by increasing the alkoxy chain length. In addition, increasing the alkoxy chain length decreases the glass transition temperature and increases the decomposition temperature of the polymers. Copyright © 2010 Elsevier Inc. All rights reserved.

[Stimulation of DNA molecules association with amphiphilic derivatives of 1,3-diazaadamantane containing hydrophobic side chanins].

PubMed

Mamaeva, O K; Gabrielian, A G; Arutiunian, G L; Bocharova, T N; Smirnova, E A; Volodin, A A; Shchelkina, A K; Kaliuzhnyĭ, D N

2014-01-01

Earlier, a new class of compounds--amphiphilic derivatives of 1,3-diazaadamantanes, capable of facilitating the strand exchange in the system of short oligonucleotides was revealed. Longer hydrophobic side chains of 1,3-diazaadamantanes promoted stronger acceleration of the reaction. In this study, interaction with DNA of two 1,3-diazaadamantane derivatives containing different side chains was investigated by use of optical methods. Concentration of the investigated 1,3-diazaadamantans micelles formation were determined by the means of monitoring fluorescence intensity enhancement of 1-anilinonaphtalene-8-sulphonate probe; as well as the ranges of concentrations where the compounds/water mixtures existed as true solutions. 1,3-diazaadamantanes affinity to DNA was determined with Fluorescent Intercalator Displacement (FID) approach. Significant increase in hydrodynamic volume of short DNA hairpins in the complexes with 1,3-diazaadamantanes was revealed by estimation of the fluorescence polarization of ethidium bromide probe bound to the hairpins. Intermolecular association of DNA hairpins upon binding with 1,3-diazaadamantans was confirmed by Förster resonance energy transfer in system of an equimolar mixture of fluorescently labeled with Cy-3 and Cy-5 hairpins. In this study, the number of positive charges at 1,3-diazaadamantane derivatives containing side chains of different lengths was demonstrated to affect their affinity to DNA, whereas longer length of the hydrophobic side chains ensured more efficient interaction between the DNA duplexes that may facilitate, in particular, DNA strand exchange.

Mapping bright and dark modes in gold nanoparticle chains using electron energy loss spectroscopy.

PubMed

Barrow, Steven J; Rossouw, David; Funston, Alison M; Botton, Gianluigi A; Mulvaney, Paul

2014-07-09

We present a scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) investigation of gold nanosphere chains with lengths varying from 1 to 5 particles. We show localized EELS signals from the chains and identify energy-loss peaks arising due to l = 1, 2, 3, 4, and 5 plasmon modes through the use of EELS mapping. We also show the evolution of the energy of these modes as the length of a given chain increases, and we find that a chain containing N particles can accommodate at least N experimentally observable modes, in addition to the transverse mode. As the chain length is increased by the addition of one more gold particle to the chain, the new N + 1 mode becomes the highest energy mode, while the existing modes lower their energy and eventually asymptote as they delocalize along the chain. We also show that modes become increasingly difficult to detect with the EELS technique as l approaches N. The data are compared to numerical simulations.

Well-defined block copolymers for gene delivery to dendritic cells: probing the effect of polycation chain-length.

PubMed

Tang, Rupei; Palumbo, R Noelle; Nagarajan, Lakshmi; Krogstad, Emily; Wang, Chun

2010-03-03

The development of safe and efficient polymer carriers for DNA vaccine delivery requires mechanistic understanding of structure-function relationship of the polymer carriers and their interaction with antigen-presenting cells. Here we have synthesized a series of diblock copolymers with well-defined chain-length using atom transfer radical polymerization and characterized the influence of polycation chain-length on the physico-chemical properties of the polymer/DNA complexes as well as the interaction with dendritic cells. The copolymers consist of a hydrophilic poly(ethylene glycol) block and a cationic poly(aminoethyl methacrylate) (PAEM) block. The average degree of polymerization (DP) of the PAEM block was varied among 19, 39, and 75, with nearly uniform distribution. With increasing PAEM chain-length, polyplexes formed by the diblock copolymers and plasmid DNA had smaller average particle size and showed higher stability against electrostatic destabilization by salt and heparin. The polymers were not toxic to mouse dendritic cells (DCs) and only displayed chain-length-dependent toxicity at a high concentration (1mg/mL). In vitro gene transfection efficiency and polyplex uptake in DCs were also found to correlate with chain-length of the PAEM block with the longer polymer chain favoring transfection and cellular uptake. The polyplexes induced a modest up-regulation of surface markers for DC maturation that was not significantly dependent on PAEM chain-length. Finally, the polyplex prepared from the longest PAEM block (DP of 75) achieved an average of 20% enhancement over non-condensed anionic dextran in terms of uptake by DCs in the draining lymph nodes 24h after subcutaneous injection into mice. Insights gained from studying such structurally well-defined polymer carriers and their interaction with dendritic cells may contribute to improved design of practically useful DNA vaccine delivery systems. Copyright 2009 Elsevier B.V. All rights reserved.

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

A Motor-Driven Mechanism for Cell-Length Sensing

PubMed Central

Rishal, Ida; Kam, Naaman; Perry, Rotem Ben-Tov; Shinder, Vera; Fisher, Elizabeth M.C.; Schiavo, Giampietro; Fainzilber, Mike

2012-01-01

Summary Size homeostasis is fundamental in cell biology, but it is not clear how large cells such as neurons can assess their own size or length. We examined a role for molecular motors in intracellular length sensing. Computational simulations suggest that spatial information can be encoded by the frequency of an oscillating retrograde signal arising from a composite negative feedback loop between bidirectional motor-dependent signals. The model predicts that decreasing either or both anterograde or retrograde signals should increase cell length, and this prediction was confirmed upon application of siRNAs for specific kinesin and/or dynein heavy chains in adult sensory neurons. Heterozygous dynein heavy chain 1 mutant sensory neurons also exhibited increased lengths both in vitro and during embryonic development. Moreover, similar length increases were observed in mouse embryonic fibroblasts upon partial downregulation of dynein heavy chain 1. Thus, molecular motors critically influence cell-length sensing and growth control. PMID:22773964

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation

NASA Astrophysics Data System (ADS)

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-01

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ˜ cs-0.5 as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

Flexible polyelectrolyte chain in a strong electrolyte solution: Insight into equilibrium properties and force-extension behavior from mesoscale simulation.

PubMed

Malekzadeh Moghani, Mahdy; Khomami, Bamin

2016-01-14

Macromolecules with ionizable groups are ubiquitous in biological and synthetic systems. Due to the complex interaction between chain and electrostatic decorrelation lengths, both equilibrium properties and micro-mechanical response of dilute solutions of polyelectrolytes (PEs) are more complex than their neutral counterparts. In this work, the bead-rod micromechanical description of a chain is used to perform hi-fidelity Brownian dynamics simulation of dilute PE solutions to ascertain the self-similar equilibrium behavior of PE chains with various linear charge densities, scaling of the Kuhn step length (lE) with salt concentration cs and the force-extension behavior of the PE chain. In accord with earlier theoretical predictions, our results indicate that for a chain with n Kuhn segments, lE ∼ cs (-0.5) as linear charge density approaches 1/n. Moreover, the constant force ensemble simulation results accurately predict the initial non-linear force-extension region of PE chain recently measured via single chain experiments. Finally, inspired by Cohen's extraction of Warner's force law from the inverse Langevin force law, a novel numerical scheme is developed to extract a new elastic force law for real chains from our discrete set of force-extension data similar to Padè expansion, which accurately depicts the initial non-linear region where the total Kuhn length is less than the thermal screening length.

Long-distance entanglement and quantum teleportation in XX spin chains

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

Campos Venuti, L.; Giampaolo, S. M.; CNR-INFM Coherentia, Napoli

2007-11-15

Isotropic XX models of one-dimensional spin-1/2 chains are investigated with the aim to elucidate the formal structure and the physical properties that allow these systems to act as channels for long-distance, high-fidelity quantum teleportation. We introduce two types of models: (i) open, dimerized XX chains, and (ii) open XX chains with small end bonds. For both models we obtain the exact expressions for the end-to-end correlations and the scaling of the energy gap with the length of the chain. We determine the end-to-end concurrence and show that model (i) supports true long-distance entanglement at zero temperature, while model (ii) supportsmore » 'quasi-long-distance' entanglement that slowly falls off with the size of the chain. Due to the different scalings of the gaps, respectively exponential for model (i) and algebraic in model (ii), we demonstrate that the latter allows for efficient qubit teleportation with high fidelity in sufficiently long chains even at moderately low temperatures.« less

Critical effects of alkyl chain length on fibril structures in benzene-trans(RR)- or (SS)-N,N'-alkanoyl-1,2-diaminocyclohexane gels.

PubMed

Sato, Hisako; Nakae, Takahiro; Morimoto, Kazuya; Tamura, Kenji

2012-02-28

Vibrational circular dichroism (VCD) spectra were recorded on benzene-d(6) gels formed by chiral low molecular mass gelators (LMGs), trans(RR)- or trans(SS)-N,N'-alkanoyl-1,2-diaminocyclohexane (denoted by RR-C(n) or SS-C(n), respectively; n = the number of carbon atoms in an introduced alkanoyl group). Attention was focused on the effects of alkyl chain length on the structures of the gels. When n was changed from 6 to 12, the signs of the coupled peaks around 1550 cm(-1) in the VCD spectra, which were assigned to the symmetric and asymmetric C=O stretching vibrations from the higher to lower wavenumber, respectively, critically depended on the alkyl chain length. In the case of RR-C(n), for example, the signs of the couplet were plus and minus for n = 8, 9, 10 and 12, while the signs of the same couplet were reversed for n = 6 and 7. The conformations of LMGs in fibrils were determined by comparing the observed IR and VCD spectra with those calculated for a monomeric molecule. The observed reversal of signs in the C=O couplet was rationalized in terms of the different modes of hydrogen bonding. In the case of C(8), C(9), C(10) and C(12), gelator molecules were stacked with their cyclohexyl rings in parallel, forming double anti-parallel chains of intermolecular hydrogen bonds using two pairs of >NH and >C=O groups. In case of C(6) and C(7), gelator molecules were stacked through a single chain of intermolecular hydrogen bonds using a pair of >NH and >C=O groups. The remaining pair of >NH and >C=O groups formed an intramolecular hydrogen bond.

Structural requirements for the cytoprotective actions of mono-unsaturated fatty acids in the pancreatic β-cell line, BRIN-BD11

PubMed Central

Dhayal, S; Welters, H J; Morgan, N G

2008-01-01

Background and purpose: Exposure of pancreatic β-cells to long-chain free fatty acids leads to differential responses according to the chain length and degree of unsaturation. In particular, long-chain saturated molecules such as palmitate (C16:0) cause apoptosis, whereas equivalent mono-unsaturated species (for example, palmitoleate (C16:1)) are not overtly toxic. Moreover, mono-unsaturates exert a powerful cytoprotective response against a range of proapoptotic stimuli. However, the structural requirements that determine cytoprotection have not been determined and form the basis of the present study. Experimental approach: BRIN-BD11 and INS-1 β-cells were exposed either to the saturated fatty acid palmitate, or to serum withdrawal, to mediate cytotoxicity. The protective effects of a wide range of mono-unsaturated fatty acid derivatives were tested in cytotoxicity assays. Effector caspase activity was also measured and correlated with viability. Key results: The cytotoxic actions of palmitate were inhibited dose-dependently by long-chain mono-unsaturated fatty acids with a defined potency order C18:1>C16:1≫C14:1. The configuration of the double bond was also important with cis forms being more potent than trans forms. Alkylated mono-unsaturated fatty-acid derivates were also cytoprotective, although their efficacy declined as the alkyl chain length increased. Cytoprotection was achieved rapidly on addition of mono-unsaturates and correlated with a rapid and dramatic inhibition of caspase-3/7 activity in palmitate-treated cells. Conclusions and implications: The data reveal the structural requirements that dictate the cytoprotective actions of mono-unsaturated fatty acids in pancreatic β-cells. Metabolic activation is not required and the data point at the potential involvement of a fatty acid receptor in mediating cytoprotection. PMID:18297101

Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

PubMed

Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

2017-03-15

The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization.

PubMed

deRonde, Brittany M; Posey, Nicholas D; Otter, Ronja; Caffrey, Leah M; Minter, Lisa M; Tew, Gregory N

2016-06-13

Exploring the role of polymer structure for the internalization of biologically relevant cargo, specifically siRNA, is of critical importance to the development of improved delivery reagents. Herein, we report guanidinium-rich protein transduction domain mimics (PTDMs) based on a ring-opening metathesis polymerization scaffold containing tunable hydrophobic moieties that promote siRNA internalization. Structure-activity relationships using Jurkat T cells and HeLa cells were explored to determine how the length of the hydrophobic block and the hydrophobic side chain compositions of these PTDMs impacted siRNA internalization. To explore the hydrophobic block length, two different series of diblock copolymers were synthesized: one series with symmetric block lengths and one with asymmetric block lengths. At similar cationic block lengths, asymmetric and symmetric PTDMs promoted siRNA internalization in the same percentages of the cell population regardless of the hydrophobic block length; however, with 20 repeat units of cationic charge, the asymmetric block length had greater siRNA internalization, highlighting the nontrivial relationships between hydrophobicity and overall cationic charge. To further probe how the hydrophobic side chains impacted siRNA internalization, an additional series of asymmetric PTDMs was synthesized that featured a fixed hydrophobic block length of five repeat units that contained either dimethyl (dMe), methyl phenyl (MePh), or diphenyl (dPh) side chains and varied cationic block lengths. This series was further expanded to incorporate hydrophobic blocks consisting of diethyl (dEt), diisobutyl (diBu), and dicyclohexyl (dCy) based repeat units to better define the hydrophobic window for which our PTDMs had optimal activity. High-performance liquid chromatography retention times quantified the relative hydrophobicities of the noncationic building blocks. PTDMs containing the MePh, diBu, and dPh hydrophobic blocks were shown to have superior siRNA internalization capabilities compared to their more and less hydrophobic counterparts, demonstrating a critical window of relative hydrophobicity for optimal internalization. This better understanding of how hydrophobicity impacts PTDM-induced internalization efficiencies will help guide the development of future delivery reagents.

Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods

DOE PAGES

Motta, Mario; Ceperley, David M.; Chan, Garnet Kin-Lic; ...

2017-09-28

We present numerical results for the equation of state of an infinite chain of hydrogen atoms. A variety of modern many-body methods are employed, with exhaustive cross-checks and validation. Approaches for reaching the continuous space limit and the thermodynamic limit are investigated, proposed, and tested. The detailed comparisons provide a benchmark for assessing the current state of the art in many-body computation, and for the development of new methods. The ground-state energy per atom in the linear chain is accurately determined versus bond length, with a confidence bound given on all uncertainties.

Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods

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

Motta, Mario; Ceperley, David M.; Chan, Garnet Kin-Lic

We present numerical results for the equation of state of an infinite chain of hydrogen atoms. A variety of modern many-body methods are employed, with exhaustive cross-checks and validation. Approaches for reaching the continuous space limit and the thermodynamic limit are investigated, proposed, and tested. The detailed comparisons provide a benchmark for assessing the current state of the art in many-body computation, and for the development of new methods. The ground-state energy per atom in the linear chain is accurately determined versus bond length, with a confidence bound given on all uncertainties.

Light, nutrients, and food-chain length constrain planktonic energy transfer efficiency across multiple trophic levels

PubMed Central

Dickman, Elizabeth M.; Newell, Jennifer M.; González, María J.; Vanni, Michael J.

2008-01-01

The efficiency of energy transfer through food chains [food chain efficiency (FCE)] is an important ecosystem function. It has been hypothesized that FCE across multiple trophic levels is constrained by the efficiency at which herbivores use plant energy, which depends on plant nutritional quality. Furthermore, the number of trophic levels may also constrain FCE, because herbivores are less efficient in using plant production when they are constrained by carnivores. These hypotheses have not been tested experimentally in food chains with 3 or more trophic levels. In a field experiment manipulating light, nutrients, and food-chain length, we show that FCE is constrained by algal food quality and food-chain length. FCE across 3 trophic levels (phytoplankton to carnivorous fish) was highest under low light and high nutrients, where algal quality was best as indicated by taxonomic composition and nutrient stoichiometry. In 3-level systems, FCE was constrained by the efficiency at which both herbivores and carnivores converted food into production; a strong nutrient effect on carnivore efficiency suggests a carryover effect of algal quality across 3 trophic levels. Energy transfer efficiency from algae to herbivores was also higher in 2-level systems (without carnivores) than in 3-level systems. Our results support the hypothesis that FCE is strongly constrained by light, nutrients, and food-chain length and suggest that carryover effects across multiple trophic levels are important. Because many environmental perturbations affect light, nutrients, and food-chain length, and many ecological services are mediated by FCE, it will be important to apply these findings to various ecosystem types. PMID:19011082

Broken Chains and Reneging: A Review of 1748 Kidney Paired Donation Transplants.

PubMed

Cowan, N; Gritsch, H A; Nassiri, N; Sinacore, J; Veale, J

2017-09-01

Concerns regarding the potential for broken chains and "reneges" within kidney paired donation (KPD) and its effect on chain length have been raised previously. Although these concerns have been tested in simulation studies, real-world data have yet to be evaluated. The purpose of this study was to evaluate the actual rate and causes of broken chains within a large KPD program. All patients undergoing renal transplantation through the National Kidney Registry from 2008 through May 2016 were included for analysis. Broken chains and loops were identified. A total of 344 chains and 78 loops were completed during the study period, yielding a total of 1748 transplants. Twenty broken chains and one broken loop were identified. The mean chain length (number of transplants) within broken chains was 4.8 compared with 4.6 of completed chains (p = 0.78). The most common causes of a broken chain were donor medical issues incurred while acting as a bridge donor (n = 8), donors electing not to proceed (n = 6), and kidneys being declined by the recipient surgeon (n = 4). All recipients involved in a broken chain subsequently received a transplant. Based on the results, broken chains are infrequent, are rarely due to lack of donor motivation, and have no significant impact on chain length. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

The importance of chain length for the polyphosphate enhancement of acidic potassium permanganate chemiluminescence.

PubMed

Holland, Brendan J; Adcock, Jacqui L; Nesterenko, Pavel N; Peristyy, Anton; Stevenson, Paul G; Barnett, Neil W; Conlan, Xavier A; Francis, Paul S

2014-09-09

Sodium polyphosphate is commonly used to enhance chemiluminescence reactions with acidic potassium permanganate through a dual enhancement mechanism, but commercially available polyphosphates vary greatly in composition. We have examined the influence of polyphosphate composition and concentration on both the dual enhancement mechanism of chemiluminescence intensity and the stability of the reagent under analytically useful conditions. The average chain length (n) provides a convenient characterisation, but materials with similar values can exhibit markedly different distributions of phosphate oligomers. There is a minimum polyphosphate chain length (∼6) required for a large enhancement of the emission intensity, but no further advantage was obtained using polyphosphate materials with much longer average chain lengths. Providing there is a sufficient average chain length, the optimum concentration of polyphosphate is dependent on the analyte and in some cases, may be lower than the quantities previously used in routine detection. However, the concentration of polyphosphate should not be lowered in permanganate reagents that have been partially reduced to form high concentrations of the key manganese(III) co-reactant, as this intermediate needs to be stabilised to prevent formation of insoluble manganese(IV). Copyright © 2014 Elsevier B.V. All rights reserved.

Insights into the structural and physicochemical properties of small granular starches from two hydrophyte duckweeds, Spirodela oligorrhiza and Lemna minor.

PubMed

Chen, Lei; Yu, Changjiang; Ma, Yubin; Xu, Hua; Wang, Shumin; Wang, Yu; Liu, Xingxun; Zhou, Gongke

2016-11-29

The structure and physicochemical properties of starches from two hydrophyte duckweeds, Spirodela oligorrhiza and Lemna minor, were investigated and compared in this study. The amylose content and average size of starches were determined to be 20.85%, 4.70 μm and 27.77%, 6.17 μm for Spirodela oligorrhiza and Lemna minor, respectively. The average chain length of two duckweed starches was measured to be around DP 28. The chain length distribution was observed to be greatly different from other reported starches for the high proportion of long chains (DP ≥ 37) over 50%. Wide-angle X-ray diffraction profiles of the two starch samples displayed typical B-type diffraction pattern. The gelatinization enthalpy-changes (ΔH gel ) of two starch samples was about 10.40 J/g for two duckweed starches. The present results suggested the potential utilization of small granular starches from duckweed in functional foods and dietary supplement products. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Cuphea beta-ketoacyl-ACP synthase shifts the synthesis of fatty acids towards shorter chains in Arabidopsis seeds expressing Cuphea FatB thioesterases.

PubMed

Leonard, J M; Knapp, S J; Slabaugh, M B

1998-03-01

Acyl-acyl carrier protein (ACP) thioesterases with specificities on medium chain substrates (C8-C14) are requisite enzymes in plants that produce 8:0, 10:0, 12:0 and 14:0 seed oils, but they may not be the sole enzymatic determinants of chain length. The contribution to chain length regulation of a beta-ketoacyl-ACP synthase, Cw KAS A1, derived from Cuphea wrightii, a species that accumulates 30% 10:0 and 54% 12:0 in seed oils, was investigated. Expression of Cw KAS A1 in Arabidopsis seeds reduced 16:0 from 8.2 to 6.2 mol%, suggesting a KAS II-type activity. In the presence of the KAS I inhibitor cerulenin, however, transgenic seed extracts extended 6:0- and 8:0-ACP at a rate four- to fivefold greater than extracts from untransformed plants, whereas no difference was observed in extension of 14:0- and 16:0-ACP. The effect of KAS A1 on seed oils was tested by combining it with the C. wrightii medium chain-specific thioesterases, Cw FatB1 and Cw FatB2, in crosses of transformed plants. Fatty acid synthesis thesis shifted towards shorter chains in progeny expressing both classes of enzymes. KasA1/FatB1 homozygotes produced threefold more 12:0 than the FatB1 parent while 14:0 and 16:0 were reduced by one-third and one-half, respectively. F2 progeny expressing KasA1 and FatB2 produced twofold more 10:0 and 1.4-fold more 12:0 than the FatB2 parent, and the double-transgenic progeny produced one-quarter less 14:0 and one-half less 16:0 than the FatB2 parent. It is hypothesized that the shift towards production of shorter chains resulted from increased pools of medium chain acyl-ACP resulting from KAS A1 activity. The combined activities of KAS A1 and FatB thioesterases appear to determine the C. wrightii phenotype.

ε-Poly-l-Lysine Peptide Chain Length Regulated by the Linkers Connecting the Transmembrane Domains of ε-Poly-l-Lysine Synthetase

PubMed Central

Kito, Naoko; Kita, Akihiro; Imokawa, Yuuki; Yamanaka, Kazuya; Maruyama, Chitose; Katano, Hajime

2014-01-01

ε-Poly-l-lysine (ε-PL), consisting of 25 to 35 l-lysine residues with linkages between the α-carboxyl groups and ε-amino groups, is produced by Streptomyces albulus NBRC14147. ε-PL synthetase (Pls) is a membrane protein with six transmembrane domains (TM1 to TM6) as well as both an adenylation domain and a thiolation domain, characteristic of the nonribosomal peptide synthetases. Pls directly generates ε-PL chain length diversity (25- to 35-mer), but the processes that control the chain length of ε-PL during the polymerization reaction are still not fully understood. Here, we report on the identification of Pls amino acid residues involved in the regulation of the ε-PL chain length. From approximately 12,000 variants generated by random mutagenesis, we found 8 Pls variants that produced shorter chains of ε-PL. These variants have one or more mutations in two linker regions connecting the TM1 and TM2 domains and the TM3 and TM4 domains. In the Pls catalytic mechanism, the growing chain of ε-PL is not tethered to the enzyme, implying that the enzyme must hold the growing chain until the polymerization reaction is complete. Our findings reveal that the linker regions are important contributors to grasp the growing chain of ε-PL. PMID:24907331

Monte Carlo simulations of lattice models for single polymer systems

NASA Astrophysics Data System (ADS)

Hsu, Hsiao-Ping

2014-10-01

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N ˜ O(10^4). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and sqrt{10}, we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.

Microplate Bioassay for Determining Substrate Selectivity of "Candida rugosa" Lipase

ERIC Educational Resources Information Center

Wang, Shi-zhen; Fang, Bai-shan

2012-01-01

Substrate selectivity of "Candida rugosa" lipase was tested using "p"-nitrophenyl esters of increasing chain length (C[subscript 1], C[subscript 7], C[subscript 15]) using the high-throughput screening method. A fast and easy 96-well microplate bioassay was developed to help students learn and practice biotechnological specificity screen. The…

Qualitative variation in proanthocyanidin composition of Populus species and hybrids: genetics is the key.

PubMed

Scioneaux, Ashley N; Schmidt, Michael A; Moore, Melissa A; Lindroth, Richard L; Wooley, Stuart C; Hagerman, Ann E

2011-01-01

The literature on proanthocyanidins (tannins) in ecological systems is dominated by quantitative studies. Despite evidence that the qualitative characteristics (subunit type, polymer chain length) of these complex polyphenolics are important determinants of biological activity, little is known about genetic and environmental controls on the type of proanthocyanidins produced by plants. We tested the hypothesis that genetics, season, developmental stage, and environment determine proanthocyanidin qualitative characteristics by using four Populus "cross types" (narrowleaf [P. angustifolia], Fremont [P. fremontii], F1 hybrids, and backcrosses to narrowleaf). We used thiolysis and HPLC analysis to characterize the proanthocyanidins, and found that genetics strongly control composition. The narrowleaf plants accumulate mixed procyanidin/prodelphinidins with average composition epicatechin(11)-epigallocatechin(8)-catechin(2)-catechin((terminal)). Backcross genotypes produce mixed procyanidin/prodelphinidins similar to narrowleaf, while Fremont makes procyanidin dimers, and the F1 plants contain procyanidin heptamers. Less striking effects were noted for genotype × environment, while season and developmental zone had little effect on proanthocyanidin composition or chain length. We discuss the metabolic and ecological consequences of differences in condensed tannin qualitative traits.

Microphase separation of comb copolymers with two different lengths of side chains

NASA Astrophysics Data System (ADS)

Aliev, M. A.; Kuzminyh, N. Yu.

2009-10-01

The phase behavior of the monodisperse AB comb copolymer melt contained the macromolecules of special architecture is discussed. Each macromolecule is assumed to be composed of two comb blocks which differ in numbers of side chains and numbers of monomer units in these chains. It is shown (by analysis of the structure factor of the melt) that microphase separation at two different length scales in the melt is possible. The large and small length scales correspond to separation between comb blocks and separation between monomer units in repeating fragments of blocks, respectively. The classification diagrams indicated which length scale is favored for a given parameters of chemical structure of macromolecules are constructed.

Twist-writhe partitioning in a coarse-grained DNA minicircle model

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan

2010-04-01

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

Elongated phytoglycogen chain length in transgenic rice endosperm expressing active starch synthase IIa affects the altered solubility and crystallinity of the storage α-glucan

PubMed Central

Fujita, Naoko; Toyosawa, Yoshiko; Utsumi, Yoshinori

2012-01-01

The relationship between the solubility, crystallinity, and length of the unit chains of plant storage α-glucan was investigated by manipulating the chain length of α-glucans accumulated in a rice mutant. Transgenic lines were produced by introducing a cDNA for starch synthase IIa (SSIIa) from an indica cultivar (SSIIa I, coding for active SSIIa) into an isoamylase1 (ISA1)-deficient mutant (isa1) that was derived from a japonica cultivar (bearing inactive SSIIa proteins). The water-soluble fraction accounted for >95% of the total α-glucan in the isa1 mutant, whereas it was only 35–70% in the transgenic SSIIa I /isa1 lines. Thus, the α-glucans from the SSIIa I /isa1 lines were fractionated into soluble and insoluble fractions prior to the following characterizations. X-ray diffraction analysis revealed a weak B-type crystallinity for the α-glucans of the insoluble fraction, while no crystallinity was confirmed for α-glucans in isa1. Concerning the degree of polymerization (DP) ≤30, the chain lengths of these α-glucans differed significantly in the order of SSIIa I /isa1 insoluble > SSIIa I /isa1 soluble > α-glucans in isa1. The amount of long chains with DP ≥33 was higher in the insoluble fraction α-glucans than in the other two α-glucans. No difference was observed in the chain length distributions of the β-amylase limit dextrins among these α-glucans. These results suggest that in the SSIIa I /isa1 transgenic lines, the unit chains of α-glucans were elongated by SSIIaI, whereas the expression of SSIIaI did not affect the branch positions. Thus, the observed insolubility and crystallinity of the insoluble fraction can be attributed to the elongated length of the outer chains due to SSIIaI. PMID:23048127

The electrostatic persistence length of polymers beyond the OSF limit.

PubMed

Everaers, R; Milchev, A; Yamakov, V

2002-05-01

We use large-scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length l(e) of isolated, uniformly charged polymers with Debye-Hückel intrachain interactions in the limit where the screening length kappa(-1) exceeds the intrinsic persistence length of the chains. Our simulations cover a significantly larger part of the parameter space than previous studies. We observe no significant deviations from the prediction l(e) proportional to kappa(-2) by Khokhlov and Khachaturian which is based on applying the Odijk-Skolnick-Fixman theories of electrostatic bending rigidity and electrostatically excluded volume to the stretched de Gennes-Pincus-Velasco-Brochard polyelectrolyte blob chain. A linear or sublinear dependence of the persistence length on the screening length can be ruled out. We show that previous results pointing into this direction are due to a combination of excluded-volume and finite chain length effects. The paper emphasizes the role of scaling arguments in the development of useful representations for experimental and simulation data.

Effects of Chain Length and Saturability of Fatty Acids on Phospholipids and Proteins in Plasma Membranes of Bovine Mammary Gland.

PubMed

Yan, Qiongxian; Tang, Shaoxun; Han, Xuefeng; Bamikole, Musibau Adungbe; Zhou, Chuanshe; Kang, Jinhe; Wang, Min; Tan, Zhiliang

2016-12-01

Free fatty acids (FFAs) in plasma are essential substrates for de novo synthesis of milk fat, or directly import into mammary cells. The physico-chemical properties of mammary cells membrane composition affected by FFAs with different chain lengths and saturability are unclear yet. Employing GC, FTIR and fluorescence spectroscopy, the adsorption capacity, phospholipids content, membrane proteins conformation, lipid peroxidation product, and free sulfhydryl of plasma membranes (PMs) interacted with different FFAs were determined. The mammary cells PMs at 38 and 39.5 °C showed different adsorption capacities: acetic acid (Ac) > stearic acid (SA) > β-hydroxybutyric acid (BHBA) > trans10, cis12 CLA. In the FTIR spectrum, the major adsorption peaks appeared at 2920 and 2850 cm -1 for phospholipids, and at 1628 and 1560 cm -1 for membrane proteins. The intensities of PMs-FFAs complexes were varied with the FFAs species and their initial concentrations. The β-sheet and turn structures of membrane proteins were transferred into random coil and α-helix after BHBA, SA and trans10, cis12 CLA treatments compared with Ac treatment. The quenching effects on the fluorescence of endogenous membrane protein, 1, 8-ANS, NBD-PE, and DHPE entrapped in PMs by LCFA were different from those of short chain FFAs. These results indicate that the adsorption of FFAs could change membrane protein conformation and polarity of head group in phospholipids. This variation of the mammary cells PMs was regulated by carbon chain length and saturability of FFAs.

Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations.

PubMed

Nakano, Miki; Ebina, Kuniyoshi; Tanaka, Shigenori

2013-04-01

Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.

Influence of phosphocholine alkyl chain length on peptide-micelle interactions and micellar size and shape.

PubMed

Göbl, Christoph; Dulle, Martin; Hohlweg, Walter; Grossauer, Jörg; Falsone, S Fabio; Glatter, Otto; Zangger, Klaus

2010-04-08

The interaction with biological membranes is of functional importance for many peptides and proteins. Structural studies on such membrane-bound biomacromolecules are often carried out in solutions containing small membrane-mimetic assemblies of detergent molecules. To investigate the influence of the hydrophobic chain length on the structure, diffusional and dynamical behavior of a peptide bound to micelles, we studied the binding of three peptides to n-phosphocholines with n ranging from 8 to 16. The peptides studied are the 15 residue antimicrobial peptide CM15, the 25-residue transmembrane helix 7 of yeast V-ATPase (TM7), and the 35-residue bacterial toxin LdrD. To keep the dimension of the peptide-membrane-mimetic assembly small, micelles are typically used when studying membrane-bound peptides and proteins, for example, by solution NMR spectroscopy. Since they are readily available in deuterated form most often sodium-dodecylsulfate (SDS) and dodecylphosphocholine (DPC) are used as the micelle-forming detergent. Using NMR, CD, and SAXS, we found that all phosphocholines studied form spherical micelles in the presence and absence of small bound peptides and the diameters of the micelles are basically unchanged upon peptide binding. The size of the peptide relative to the micelle determines to what extent the secondary structure can form. For small peptides (up to approximately 25 residues) the use of shorter chain phosphocholines is recommended for solution NMR studies due to the favorable spectral quality and since they are as well-structured as in DPC. In contrast, larger peptides are better structured in micelles formed by detergents with chain lengths longer than DPC.

Active microrheology of entangled biopolymer composites link polymer flexibility and length to molecular force response

NASA Astrophysics Data System (ADS)

Fitzpatrick, Robert; Hauer, Cole; Kyrillos, Carl; McGorty, Ryan; Robertson-Anderson, Rae

Entangled polymers have complex viscoelastic properties that are tuned by polymer lengths and flexibilities. Entangled composites of distinct polymers offer added versatility and display nonlinear mechanics, serving as a platform for multifunctional materials. To determine the role of flexibility and length in polymer composites we use optical tweezers and confocal microscopy to measure mechanical and structural properties of co-entangled actin and DNA. Actin filaments have lengths of 5-20 μm, comparable to their persistence length, while DNA of similar lengths have hundreds of persistence lengths per chain. To characterize the nonlinear mechanics of actin-DNA composites, we optically drive a microsphere through the composite and measure the induced force during and following strain. We characterize viscoelasticity and relaxation timescales; and determine the dependence of these quantities on the actin:DNA ratio (0:1-1:0) and DNA length (4-100 μm). We use confocal microscopy to image distinctly labeled co-entangled actin and DNA and characterize network homogeneity and fluctuations. Initial results show actin and DNA are well-integrated and form structurally homogenous networks that exhibit stiffness and relaxation times that increase nonlinearly with increased actin. NSF Career Award (DMR-1254340), AFOSR Young Investigator Program Award (FA95550-12-1-0315), Scialog Collaborative Innovation Award funed by Research Corp. for Scientific Advancement (24192).

How ionic species structure influences phase structure and transitions from protic ionic liquids to liquid crystals to crystals.

PubMed

Greaves, Tamar L; Broomhall, Hayden; Weerawardena, Asoka; Osborne, Dale A; Canonge, Bastien A; Drummond, Calum J

2017-12-14

The phase behaviour of n-alkylammonium (C6 to C16) nitrates and formates has been characterised using synchrotron small angle and wide angle X-ray scattering (SAXS/WAXS), differential scanning calorimetry (DSC), cross polarised optical microscopy (CPOM) and Fourier transform infrared spectroscopy (FTIR). The protic salts may exist as crystalline, liquid crystalline or ionic liquid materials depending on the alkyl chain length and temperature. n-Alkylammonium nitrates with n ≥ 6 form thermotropic liquid crystalline (LC) lamellar phases, whereas n ≥ 8 was required for the formate series to form this LC phase. The protic ionic liquid phase showed an intermediate length scale nanostructure resulting from the segregation of the polar and nonpolar components of the ionic liquid. This segregation was enhanced for longer n-alkyl chains, with a corresponding increase in the correlation length scale. The crystalline and liquid crystalline phases were both lamellar. Phase transition temperatures, lamellar d-spacings, and liquid correlation lengths for the n-alkylammonium nitrates and formates were compared with those for n-alkylammonium chlorides and n-alkylamines. Plateau regions in the liquid crystalline to liquid phase transition temperatures as a function of n for the n-alkylammonium nitrates and formates are consistent with hydrogen-bonding and cation-anion interactions between the ionic species dominating alkyl chain-chain van der Waals interactions, with the exception of the mid chained hexyl- and heptylammonium formates. The d-spacings of the lamellar phases for both the n-alkylammonium nitrates and formates were consistent with an increase in chain-chain layer interdigitation within the bilayer-based lamellae with increasing alkyl chain length, and they were comparable to the n-alkylammonium chlorides.

Effects of alkyl chain length and solvents on thermodynamic dissociation constants of the ionic liquids with one carboxyl group in the alkyl chain of imidazolium cations.

PubMed

Chen, Yuehua; Wang, Huiyong; Wang, Jianji

2014-05-01

Thermodynamic dissociation constants of the Brønsted acidic ionic liquids (ILs) are important for their catalytic and separation applications. In this work, a series of imidazolium bromides with one carboxylic acid substitute group in their alkyl chain ([{(CH2)nCOOH}mim]Br, n = 1,3,5,7) have been synthesized, and their dissociation constants (pKa) at different ionic strengths have been determined in aqueous and aqueous organic solvents at 0.1 mole fraction (x) of ethanol, glycol, iso-propanol, and dimethyl sulfoxide by potentiometric titrations at 298.2 K. The standard thermodynamic dissociation constants (pKa(T)) of the ILs in these solvents were calculated from the extended Debye-Hückel equation. It was found that the pKa values increased with the increase of ionic strength of the media and of the addition of organic solvent in water. The pKa(T) values also increased with the increase of the alkyl chain length of cations of the ILs. In addition, the effect of solvent nature on pKa(T) values is interpreted from solvation of the dissociation components and their Gibbs energy of transfer from water to aqueous organic solutions.

Physico-chemical characterization of products from vacuum oil under delayed coking process by infrared spectroscopy and chemometrics methods

NASA Astrophysics Data System (ADS)

Meléndez, L. V.; Cabanzo, R.; Mejía-Ospino, E.; Guzmán, A.

2016-02-01

Eight vacuum residues and their delayed coking liquids products from Colombian crude were study by infrared spectroscopy with attenuated total reflectance (FTIR-ATR) and principal component analysis (PCA). For the samples the structural parameters of aromaticity factor (fa), alifaticity (A2500-3100cm-1), aromatic condensation degree (GCA), length of aliphatic chains (LCA) and aliphatic chain length associated with aromatic (LACAR) were determined through the development of a methodology, which includes the previous processing of spectroscopy data, identifying the regions in the IR spectra of greatest variance using PCA and molecules patterns. The parameters were compared with the results obtained from proton magnetic resonance (1H-NMR) and 13C-NMR. The results showed the influence and correlation of structural parameters with some physicochemical properties such as API gravity, weight percent sulphur (% S) and Conradson carbon content (% CCR)

Delocalization of Coherent Triplet Excitons in Linear Rigid Rod Conjugated Oligomers.

PubMed

Hintze, Christian; Korf, Patrick; Degen, Frank; Schütze, Friederike; Mecking, Stefan; Steiner, Ulrich E; Drescher, Malte

2017-02-02

In this work, the triplet state delocalization in a series of monodisperse oligo(p-phenyleneethynylene)s (OPEs) is studied by pulsed electron paramagnetic resonance (EPR) and pulsed electron nuclear double resonance (ENDOR) determining zero-field splitting, optical spin polarization, and proton hyperfine couplings. Neither the zero-field splitting parameters nor the optical spin polarization change significantly with OPE chain length, in contrast to the hyperfine coupling constants, which showed a systematic decrease with chain length n according to a 2/(1 + n) decay law. The results provide striking evidence for the Frenkel-type nature of the triplet excitons exhibiting full coherent delocalization in the OPEs under investigation with up to five OPE repeat units and with a spin density distribution described by a nodeless particle in the box wave function. The same model is successfully applied to recently published data on π-conjugated porphyrin oligomers.

The interactions between ionic surfactants and phosphatidylcholine vesicles: Conductometry

NASA Astrophysics Data System (ADS)

Tsao, Heng-Kwong; Tseng, Wen Liang

2001-11-01

The interaction between ionic surfactants and phosphatidylcholine vesicles, which are prepared without addition of buffer and salt, is investigated by conductivity measurements. On the basis of the vesicle acting as a trap of charge carriers, the bilayer/aqueous phase partition coefficient K and the surfactant/lipid molar ratio Re of nine surfactants are determined. The thermodynamic consistency is satisfied by the measured parameters. The effects of the alkyl chain length (C10-C16) and ionic head group are then studied. The inverse partition coefficient K-1 is linearly related to the critical micelle concentration. The solubilizing ability Reb is a consequence of the competition between the surfactant incorporation into the bilayer and the formation of micelles. Consequently, the K parameter rises whereas the Reb parameter declines as the chain length is increased. The influence due to addition of salt is also discussed.

Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

Adsorption of small hydrocarbons on rutile TiO2(110)

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

Chen, Long; Smith, R. Scott; Kay, Bruce D.

2016-08-01

Temperature programmed desorption and molecular beam scattering were used to study the adsorption and desorption of small hydrocarbons (n-alkanes, 1-alkenes and 1-alkynes with 1 - 4 carbon atoms of C1-C4) on rutile TiO2(110). We show that the sticking coefficients for all the hydrocarbons are close to unity (> 0.95) at an adsorption temperature of 60 K. The desorption energies for hydrocarbons of the same chain length increase from n-alkanes to 1-alkenes and to 1-alkynes. This trend is likely a consequence of an additional dative bonding of the alkene and alkyne π system to the coordinatively unsaturated Ti5c sites. Similar tomore » previous studies on the adsorption of n-alkanes on metal and metal oxide surfaces, we find the desorption energies within each group (n-alkanes vs. 1-alkenes vs. 1-alkynes) from Ti5c sites increase linearly with the chain length. The absolute saturation coverages of each hydrocarbon on Ti5c sites were also determined. The saturation coverage of CH4, is found to be ~ 2/3 monolayer (ML). The saturation coverages of C2-C4 hydrocarbons are found nearly independent of the chain length with values of ~1/2 ML for n-alkanes and 1-alkenes and 2/3 ML for 1-alkynes. This result is surprising considering their similar sizes.« less

Adsorption of small hydrocarbons on rutile TiO 2(110)

DOE PAGES

Chen, Long; Smith, R. Scott; Kay, Bruce D.; ...

2015-11-21

Here, temperature programmed desorption and molecular beam scattering were used to study the adsorption and desorption of small hydrocarbons (n-alkanes, 1-alkenes and 1-alkynes of C 1–C 4) on rutile TiO 2(110). We show that the sticking coefficients for all the hydrocarbons are close to unity (> 0.95) at an adsorption temperature of 60 K. The desorption energies for hydrocarbons of the same chain length increase from n-alkanes to 1-alkenes and to 1-alkynes. This trend is likely a consequence of additional dative bonding of the alkene and alkyne π system to the coordinatively unsaturated Ti 5c sites. Similar to previous studiesmore » on the adsorption of n-alkanes on metal and metal oxide surfaces, we find that the desorption energies within each group (n-alkanes vs. 1-alkenes vs. 1-alkynes) from Ti 5c sites increase linearly with the chain length. The absolute saturation coverages of each hydrocarbon on Ti 5c sites were also determined. The saturation coverage of CH 4, is found to be ~ 2/3 monolayer (ML). The saturation coverages of C 2–C 4 hydrocarbons are found nearly independent of the chain length with values of ~ 1/2 ML for n-alkanes and 1-alkenes and 2/3 ML for 1-alkynes. This result is surprising considering their similar sizes.« less

A new paradigm for the molecular basis of rubber elasticity

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

Hanson, David E.; Barber, John L.

The molecular basis for rubber elasticity is arguably the oldest and one of the most important questions in the field of polymer physics. The theoretical investigation of rubber elasticity began in earnest almost a century ago with the development of analytic thermodynamic models, based on simple, highly-symmetric configurations of so-called Gaussian chains, i.e. polymer chains that obey Markov statistics. Numerous theories have been proposed over the past 90 years based on the ansatz that the elastic force for individual network chains arises from the entropy change associated with the distribution of end-to-end distances of a free polymer chain. There aremore » serious philosophical objections to this assumption and others, such as the assumption that all network nodes undergo affine motion and that all of the network chains have the same length. Recently, a new paradigm for elasticity in rubber networks has been proposed that is based on mechanisms that originate at the molecular level. Using conventional statistical mechanics analyses, quantum chemistry, and molecular dynamics simulations, the fundamental entropic and enthalpic chain extension forces for polyisoprene (natural rubber) have been determined, along with estimates for the basic force constants. Concurrently, the complex morphology of natural rubber networks (the joint probability density distributions that relate the chain end-to-end distance to its contour length) has also been captured in a numerical model. When molecular chain forces are merged with the network structure in this model, it is possible to study the mechanical response to tensile and compressive strains of a representative volume element of a polymer network. As strain is imposed on a network, pathways of connected taut chains, that completely span the network along strain axis, emerge. Although these chains represent only a few percent of the total, they account for nearly all of the elastic stress at high strain. Here we provide a brief review of previous elasticity theories and their deficiencies, and present a new paradigm with an emphasis on experimental comparisons.« less

A new paradigm for the molecular basis of rubber elasticity

DOE PAGES

Hanson, David E.; Barber, John L.

2015-02-19

The molecular basis for rubber elasticity is arguably the oldest and one of the most important questions in the field of polymer physics. The theoretical investigation of rubber elasticity began in earnest almost a century ago with the development of analytic thermodynamic models, based on simple, highly-symmetric configurations of so-called Gaussian chains, i.e. polymer chains that obey Markov statistics. Numerous theories have been proposed over the past 90 years based on the ansatz that the elastic force for individual network chains arises from the entropy change associated with the distribution of end-to-end distances of a free polymer chain. There aremore » serious philosophical objections to this assumption and others, such as the assumption that all network nodes undergo affine motion and that all of the network chains have the same length. Recently, a new paradigm for elasticity in rubber networks has been proposed that is based on mechanisms that originate at the molecular level. Using conventional statistical mechanics analyses, quantum chemistry, and molecular dynamics simulations, the fundamental entropic and enthalpic chain extension forces for polyisoprene (natural rubber) have been determined, along with estimates for the basic force constants. Concurrently, the complex morphology of natural rubber networks (the joint probability density distributions that relate the chain end-to-end distance to its contour length) has also been captured in a numerical model. When molecular chain forces are merged with the network structure in this model, it is possible to study the mechanical response to tensile and compressive strains of a representative volume element of a polymer network. As strain is imposed on a network, pathways of connected taut chains, that completely span the network along strain axis, emerge. Although these chains represent only a few percent of the total, they account for nearly all of the elastic stress at high strain. Here we provide a brief review of previous elasticity theories and their deficiencies, and present a new paradigm with an emphasis on experimental comparisons.« less

PEGylation on mixed monolayer gold nanoparticles: Effect of grafting density, chain length, and surface curvature.

PubMed

Lin, Jiaqi; Zhang, Heng; Morovati, Vahid; Dargazany, Roozbeh

2017-10-15

PEGylation on nanoparticles (NPs) is widely used to prevent aggregation and to mask NPs from the fast clearance system in the body. Understanding the molecular details of the PEG layer could facilitate rational design of PEGylated NPs that maximize their solubility and stealth ability without significantly compromising the targeting efficiency and cellular uptake. Here, we use molecular dynamics (MD) simulation to understand the structural and dynamic the PEG coating of mixed monolayer gold NPs. Specifically, we modeled gold NPs with PEG grafting densities ranging from 0-2.76chain/nm 2 , chain length with 0-10 PEG monomers, NP core diameter from 5nm to 500nm. It is found that the area accessed by individual PEG chains gradually transits from a "mushroom" to a "brush" conformation as NP surface curvature become flatter, whereas such a transition is not evident on small NPs when grafting density increases. It is shown that moderate grafting density (∼1.0chain/nm 2 ) and short chain length are sufficient enough to prevent NPs from aggregating in an aqueous medium. The effect of grafting density on solubility is also validated by dynamic light scattering measurements of PEGylated 5nm gold NPs. With respect to the shielding ability, simulations predict that increase either grafting density, chain length, or NP diameter will reduce the accessibility of the protected content to a certain size molecule. Interestingly, reducing NP surface curvature is estimated to be most effective in promoting shielding ability. For shielding against small molecules, increasing PEG grafting density is more effective than increasing chain length. A simple model that includes these three investigated parameters is developed based on the simulations to roughly estimate the shielding ability of the PEG layer with respect to molecules of different sizes. The findings can help expand our current understanding of the PEG layer and guide rational design of PEGylated gold NPs for a particular application by tuning the PEG grafting density, chain length, and particle size. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-02-20

Quinoa starch has very small granules with unique properties. However, the molecular structure of quinoa starch remains largely unknown. In this study, composition and amylopectin molecular structure of 9 quinoa starch samples were characterised by chromatographic techniques. In particular, the amylopectin internal molecular structure, represented by φ, β-limit dextrins (LDs), was explored. Great variations in the composition and molecular structures were recorded among samples. Compared with other amylopectins, quinoa amylopectin showed a high ratio of short chain to long chains (mean:14.6) and a high percentage of fingerprint A-chains (A fp ) (mean:10.4%). The average chain length, external chain length, and internal chain length of quinoa amylopectin were 16.6, 10.6, and 5.00 glucosyl residues, respectively. Pearson correlation and principal component analysis revealed some inherent correlations among structural parameters and a similarity of different samples. Overall, quinoa amylopectins are structurally similar to that from starches with A-type polymorph such as oat and amaranth starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chain-Length-Dependent Exciton Dynamics in Linear Oligothiophenes Probed Using Ensemble and Single-Molecule Spectroscopy.

PubMed

Kim, Tae-Woo; Kim, Woojae; Park, Kyu Hyung; Kim, Pyosang; Cho, Jae-Won; Shimizu, Hideyuki; Iyoda, Masahiko; Kim, Dongho

2016-02-04

Exciton dynamics in π-conjugated molecular systems is highly susceptible to conformational disorder. Using time-resolved and single-molecule spectroscopic techniques, the effect of chain length on the exciton dynamics in a series of linear oligothiophenes, for which the conformational disorder increased with increasing chain length, was investigated. As a result, extraordinary features of the exciton dynamics in longer-chain oligothiophene were revealed. Ultrafast fluorescence depolarization processes were observed due to exciton self-trapping in longer and bent chains. Increase in exciton delocalization during dynamic planarization processes was also observed in the linear oligothiophenes via time-resolved fluorescence spectra but was restricted in L-10T because of its considerable conformational disorder. Exciton delocalization was also unexpectedly observed in a bent chain using single-molecule fluorescence spectroscopy. Such delocalization modulates the fluorescence spectral shape by attenuating the 0-0 peak intensity. Collectively, these results provide significant insights into the exciton dynamics in conjugated polymers.

Self-Assembly, Supramolecular Organization, and Phase Behavior of L-Alanine Alkyl Esters (n = 9-18) and Characterization of Equimolar L-Alanine Lauryl Ester/Lauryl Sulfate Catanionic Complex.

PubMed

Sivaramakrishna, D; Swamy, Musti J

2015-09-08

A homologous series of l-alanine alkyl ester hydrochlorides (AEs) bearing 9-18 C atoms in the alkyl chain have been synthesized and characterized with respect to self-assembly, supramolecular structure, and phase transitions. The CMCs of AEs bearing 11-18 C atoms were found to range between 0.1 and 10 mM. Differential scanning calorimetric (DSC) studies showed that the transition temperatures (Tt), enthalpies (ΔHt) and entropies (ΔSt) of AEs in the dry state exhibit odd-even alternation, with the odd-chain-length compounds having higher Tt values, but the even-chain-length homologues showing higher values of ΔHt and ΔSt. In DSC measurements on hydrated samples, carried out at pH 5.0 and pH 10.0 (where they exist in cationic and neutral forms, respectively), compounds with 13-18 C atoms in the alkyl chain showed sharp gel-to-liquid crystalline phase transitions, and odd-even alternation was not seen in the thermodynamic parameters. The molecular structure, packing properties, and intermolecular interactions of AEs with 9 and 10 C atoms in the alkyl chain were determined by single crystal X-ray diffraction, which showed that the alkyl chains are packed in a tilted interdigitated bilayer format. d-Spacings obtained from powder X-ray diffraction studies exhibited a linear dependence on the alkyl chain length, suggesting that the other AEs also adopt an interdigitated bilayer structure. Turbidimetric, fluorescence spectroscopic, and isothermal titration calorimetric (ITC) studies established that in aqueous dispersions l-alanine lauryl ester hydrochloride (ALE·HCl) and sodium dodecyl sulfate (SDS) form an equimolar complex. Transmission electron microscopic and DSC studies indicate that the complex exists as unilamellar liposomes, which exhibit a sharp phase transition at ∼39 °C. The aggregates were disrupted at high pH, suggesting that the catanionic complex would be useful to develop a base-labile drug delivery system. ITC studies indicated that ALE·HCl forms a strong complex with DNA, suggesting that the AEs may find use in DNA therapeutics as well.

Cloud point phenomena for POE-type nonionic surfactants in a model room temperature ionic liquid.

PubMed

Inoue, Tohru; Misono, Takeshi

2008-10-15

The cloud point phenomenon has been investigated for the solutions of polyoxyethylene (POE)-type nonionic surfactants (C(12)E(5), C(12)E(6), C(12)E(7), C(10)E(6), and C(14)E(6)) in 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)), a typical room temperature ionic liquid (RTIL). The cloud point, T(c), increases with the elongation of the POE chain, while decreases with the increase in the hydrocarbon chain length. This demonstrates that the solvophilicity/solvophobicity of the surfactants in RTIL comes from POE chain/hydrocarbon chain. When compared with an aqueous system, the chain length dependence of T(c) is larger for the RTIL system regarding both POE and hydrocarbon chains; in particular, hydrocarbon chain length affects T(c) much more strongly in the RTIL system than in equivalent aqueous systems. In a similar fashion to the much-studied aqueous systems, the micellar growth is also observed in this RTIL solvent as the temperature approaches T(c). The cloud point curves have been analyzed using a Flory-Huggins-type model based on phase separation in polymer solutions.

The design and analysis of mooring system

NASA Astrophysics Data System (ADS)

Li, Yixuan

2017-05-01

In this paper, the force status and a design method of single chain mooring system for shallow sea observation network are studied. With treating the link of a chain, steel drum and steel pipe as a rigid body, the recurrence model is established by using Newton's first law and the law of Moment equilibrium theorem. Via the simplified calculation of dichotomy searching, we determine the design parameters of mooring system, such as anchor model, anchor chain length, heavy ball quality under different water flow and wind conditions. We apply MATLAB to simulate the internal steady state of the system in the fixed scheme, water depth of buoy and swimming area to meet the decision-making needs, providing an idea for the actual scheme design of mooring system.

Temporary protection of metals against atmospheric corrosion by saturated straight chain aliphatic monocarboxylates. Mechanisms of inhibition

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

Kapin, C.; Steinmetz, P.; Steinmetz, J.

1998-12-31

This work was devoted to the investigations of the ability of saturated straight chain aliphatic monocarboxylates to inhibit corrosion of mild steel and zinc in aerated aqueous solutions. Performances of inhibitors were shown to be dependent on their chain length, their concentration and the immersion duration. Both crystallographic parameters and solubilities of iron and zinc carboxylates were determined. Then potential-pH diagrams of iron and zinc in water were built taking the presence of metallic soaps into account. According to these diagrams, the passivation of metals was attributed to the growth of films containing metallic soaps. This model confirms that previouslymore » proposed for inhibition of copper and magnesium by the same carboxylates.« less

ε-Poly-L-lysine peptide chain length regulated by the linkers connecting the transmembrane domains of ε-Poly-L-lysine synthetase.

PubMed

Hamano, Yoshimitsu; Kito, Naoko; Kita, Akihiro; Imokawa, Yuuki; Yamanaka, Kazuya; Maruyama, Chitose; Katano, Hajime

2014-08-01

ε-Poly-l-lysine (ε-PL), consisting of 25 to 35 l-lysine residues with linkages between the α-carboxyl groups and ε-amino groups, is produced by Streptomyces albulus NBRC14147. ε-PL synthetase (Pls) is a membrane protein with six transmembrane domains (TM1 to TM6) as well as both an adenylation domain and a thiolation domain, characteristic of the nonribosomal peptide synthetases. Pls directly generates ε-PL chain length diversity (25- to 35-mer), but the processes that control the chain length of ε-PL during the polymerization reaction are still not fully understood. Here, we report on the identification of Pls amino acid residues involved in the regulation of the ε-PL chain length. From approximately 12,000 variants generated by random mutagenesis, we found 8 Pls variants that produced shorter chains of ε-PL. These variants have one or more mutations in two linker regions connecting the TM1 and TM2 domains and the TM3 and TM4 domains. In the Pls catalytic mechanism, the growing chain of ε-PL is not tethered to the enzyme, implying that the enzyme must hold the growing chain until the polymerization reaction is complete. Our findings reveal that the linker regions are important contributors to grasp the growing chain of ε-PL. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Polyphosphate kinase: demonstration that short chain polyphosphate serves as a primer for the enzymatic synthesis of polyphosphate

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

Robinson, N.A.; Wood, H.G.

1986-05-01

Polyphosphate (poly(P)) kinase, isolated from Propionibacterium shermanii, catalyzes the following reaction: poly(P/sub n/) + ATPin equilibriumpoly(P/sub n+1/) + ADP. The authors have purified this enzyme to 90% homogeneity and have shown it to be composed of 2-3 identical subunits of M/sub r/ 80,000. Investigation of the reaction mechanism by product analysis has revealed that the elongation phase is processive whereby successive elongation occurs without release of intermediate sizes until very long chains are formed. The initiation phase of synthesis has been investigated using (/sup 32/P) poly(P) primer of chain length 11-60. It is incorporated into long chain poly(P) and themore » /sup 32/P has been shown, by use of poly(P) glucokinase, to be localized at the end of the molecule. Calculation of average chain length based upon the incorporation of /sup 32/P, however, yields a value approx.3 fold higher than the value calculated by another method using poly(P) glucokinase. This result indicates that initiation of poly(P) synthesis occurs by at least one other route which does not involve short chain poly(P) primers. The effect of temperature and concentration of poly(P) primer upon the average chain length of poly(P) synthesized was also investigated. A general trend was observed in which the chain length of the synthesized poly(P) decreased as either temperature or concentration or primer was increased.« less

Generalized theory of semiflexible polymers.

PubMed

Wiggins, Paul A; Nelson, Philip C

2006-03-01

DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biologically relevant length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific, illustrative model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by renormalization group arguments. In particular, we show that either the WLC or our present model adequately describes force-extension, solution scattering, and long-contour-length cyclization experiments, regardless of the details of DNA bend elasticity. In contrast, experiments sensitive to short-length-scale chain behavior can in principle reveal dramatic departures from the linear elastic behavior assumed in the WLC model. We demonstrate this explicitly by showing that our toy model can reproduce the anomalously large short-contour-length cyclization factors recently measured by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments.

Binding of cationic pentapeptides with modified side chain lengths to negatively charged lipid membranes: Complex interplay of electrostatic and hydrophobic interactions.

PubMed

Hoernke, Maria; Schwieger, Christian; Kerth, Andreas; Blume, Alfred

2012-07-01

Basic amino acids play a key role in the binding of membrane associated proteins to negatively charged membranes. However, side chains of basic amino acids like lysine do not only provide a positive charge, but also a flexible hydrocarbon spacer that enables hydrophobic interactions. We studied the influence of hydrophobic contributions to the binding by varying the side chain length of pentapeptides with ammonium groups starting with lysine to lysine analogs with shorter side chains, namely omithine (Orn), alpha, gamma-diaminobutyric acid (Dab) and alpha, beta-diaminopropionic acid (Dap). The binding to negatively charged phosphatidylglycerol (PG) membranes was investigated by calorimetry, FT-infrared spectroscopy (FT-IR) and monolayer techniques. The binding was influenced by counteracting and sometimes compensating contributions. The influence of the bound peptides on the lipid phase behavior depends on the length of the peptide side chains. Isothermal titration calorimetry (ITC) experiments showed exothermic and endothermic effects compensating to a different extent as a function of side chain length. The increase in lipid phase transition temperature was more significant for peptides with shorter side chains. FTIR-spectroscopy revealed changes in hydration of the lipid bilayer interface after peptide binding. Using monolayer techniques, the contributions of electrostatic and hydrophobic effects could clearly be observed. Peptides with short side chains induced a pronounced decrease in surface pressure of PG monolayers whereas peptides with additional hydrophobic interactions decreased the surface pressure much less or even lead to an increase, indicating insertion of the hydrophobic part of the side chain into the lipid monolayer.

Leaf wax n-alkane distributions in and across modern plants: Implications for paleoecology and chemotaxonomy

NASA Astrophysics Data System (ADS)

Bush, Rosemary T.; McInerney, Francesca A.

2013-09-01

Long chain (C21 to C37) n-alkanes are among the most long-lived and widely utilized terrestrial plant biomarkers. Dozens of studies have examined the range and variation of n-alkane chain-length abundances in modern plants from around the world, and n-alkane distributions have been used for a variety of purposes in paleoclimatology and paleoecology as well as chemotaxonomy. However, most of the paleoecological applications of n-alkane distributions have been based on a narrow set of modern data that cannot address intra- and inter-plant variability. Here, we present the results of a study using trees from near Chicago, IL, USA, as well as a meta-analysis of published data on modern plant n-alkane distributions. First, we test the conformity of n-alkane distributions in mature leaves across the canopy of 38 individual plants from 24 species as well as across a single growing season and find no significant differences for either canopy position or time of leaf collection. Second, we compile 2093 observations from 86 sources, including the new data here, to examine the generalities of n-alkane parameters such as carbon preference index (CPI), average chain length (ACL), and chain-length ratios for different plant groups. We show that angiosperms generally produce more n-alkanes than do gymnosperms, supporting previous observations, and furthermore that CPI values show such variation in modern plants that it is prudent to discard the use of CPI as a quantitative indicator of n-alkane degradation in sediments. We also test the hypotheses that certain n-alkane chain lengths predominate in and therefore can be representative of particular plant groups, namely, C23 and C25 in Sphagnum mosses, C27 and C29 in woody plants, and C31 in graminoids (grasses). We find that chain-length distributions are highly variable within plant groups, such that chemotaxonomic distinctions between grasses and woody plants are difficult to make based on n-alkane abundances. In contrast, Sphagnum mosses are marked by their predominance of C23 and C25, chain lengths which are largely absent in terrestrial vascular plants. The results here support the use of C23 as a robust proxy for Sphagnum mosses in paleoecological studies, but not the use of C27, C29, and C31 to separate graminoids and woody plants from one another, as both groups produce highly variable but significant amounts of all three chain lengths. In Africa, C33 and C35 chain lengths appear to distinguish graminoids from some woody plants, but this may be a reflection of the differences in rainforest and savanna environments. Indeed, variation in the abundances of long n-alkane chain lengths may be responding in part to local environmental conditions, and this calls for a more directed examination of the effects of temperature and aridity on plant n-alkane distributions in natural environments.

Theory of polyelectrolytes in solvents.

PubMed

Chitanvis, Shirish M

2003-12-01

Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

Use of stable carbon and nitrogen isotopes to trace the larval striped bass food chain in the Sacramento-San Joaquin Estuary, California, April to September 1985

USGS Publications Warehouse

Rast, Walter; Sutton, J.E.

1989-01-01

To assess one potential cause for the decline of the striped bass fishery in the Sacramento-San Joaquin Estuary, stable carbon and nitrogen isotope ratios were used to examine the trophic structures of the larval striped bass food chain, and to trace the flux of these elements through the food chain components. Study results generally confirm a food chain consisting of the elements, phytoplankton/detritus-->zooplankton/Neomysis shrimp-->larval striped bass. The stable isotope ratios generally become more positive as one progresses from the lower to the higher trophic level food chain components, and no unusual trophic structure was found in the food chain. However, the data indicate an unidentified consumer organism occupying an intermediate position between the lower and higher trophic levels of the larval striped bass food chain. Based on expected trophic interactions, this unidentified consumer would have a stable carbon isotope ratio of about 28/mil and a stable nitrogen isotope ratio of about 8/mi. Three possible feeding stages for larval striped bass also were identified, based on their lengths. The smallest length fish seem to subsist on their yolk sac remnants, and the largest length fish subsist on Neomysis shrimp and zooplankton. The intermediate-length fish represent a transition stage between primary food sources and/or use of a mixture of food sources. (USGS)

Molecular design of boronic acid-functionalized squarylium cyanine dyes for multiple discriminant analysis of sialic acid in biological samples: selectivity toward monosaccharides controlled by different alkyl side chain lengths.

PubMed

Ouchi, Kazuki; Colyer, Christa L; Sebaiy, Mahmoud; Zhou, Jin; Maeda, Takeshi; Nakazumi, Hiroyuki; Shibukawa, Masami; Saito, Shingo

2015-02-03

We designed a new series of boronic acid-functionalized squarylium cyanine dyes (SQ-BA) with different lengths of alkyl chain residues, suitable for multiple discriminant analysis (MDA) of sialic acid (Neu5Ac) in biological samples. The SQ-BA dyes form aggregates based on hydrophobic interactions, which result in quenched fluorescence in aqueous solutions. When the boronic acid binds with saccharides, the fluorescence intensity increases as a result of dissociation to the emissive monomeric complex. We inferred that different dye aggregate structures (H-aggregates and J-aggregates) were induced depending on the alkyl chain length, so that monosaccharides would be recognized in different ways (especially, multipoint interaction with J-aggregates). A distinctive emission enhancement of SQ-BA dyes with shorter-alkyl-chains in the presence of Neu5Ac was observed (2.4-fold fluorescence enhancement; with formation constant 10(1.7) M(-1)), with no such enhancement for SQ-BA dyes with longer-alkyl-chain. In addition, various enhancement factors for other monosaccharides were observed depending on the alkyl chain length. Detailed thermodynamic and NMR studies of the SQ-BA complexes revealed the unique recognition mechanism: the dye aggregate with a shorter-alkyl-chain causes the slipped parallel structure and forms a stable 2:1 complex with Neu5Ac, as distinct from longer-alkyl-chain dyes, which form a 1:1 monomeric complex. MDA using the four SQ-BA dyes was performed for human urine samples, resulting in the successful discrimination between normal and abnormal Neu5Ac levels characteristic of disease. Thus, we successfully controlled various responses to similar monosaccharides with a novel approach that chemically modified not the boronic acid moiety itself but the length of the alkyl chain residue attached to the dye in order to generate specificity.

Improved end-member characterization of modern organic matter pools in the Ohrid Basin (Albania, Macedonia) and evaluation of new palaeoenvironmental proxies

NASA Astrophysics Data System (ADS)

Holtvoeth, J.; Rushworth, D.; Imeri, A.; Cara, M.; Vogel, H.; Wagner, T.; Wolff, G. A.

2015-08-01

We present elemental, lipid biomarker and compound-specific isotope (δ13C, δ2H) data for soils and leaf litter collected in the catchment of Lake Ohrid (Albania, Macedonia), as well as macrophytes, particulate organic matter and sediments from the lake itself. Lake Ohrid provides an outstanding archive of continental environmental change of at least 1.2 M years and the purpose of our study is to ground truth organic geochemical proxies that we developed in order to study past changes in the terrestrial biome. We show that soils dominate the lipid signal of the lake sediments rather than the vegetation or aquatic biomass, while compound-specific isotopes (δ13C, δ2H) determined for n-alkanoic acids confirm a dominant terrestrial source of organic matter to the lake. There is a strong imprint of suberin monomers on the composition of total lipid extracts and chain-length distributions of n-alkanoic acids, n-alcohols, ω-hydroxy acids and α,ω-dicarboxylic acids. Our end-member survey identifies that ratios of mid-chain length suberin-derived to long-chain length cuticular-derived alkyl compounds as well as their average chain length distributions can be used as new molecular proxies of organic matter sources to the lake. We tested these for the 8.2 ka event, a pronounced and widespread Holocene climate fluctuation. In SE Europe climate became drier and cooler in response to the event, as is clearly recognizable in the carbonate and organic carbon records of Lake Ohrid sediments. Our new proxies indicate biome modification in response to hydrological changes, identifying two phases of increased soil OM supply, first from topsoils and then from mineral soils. Our study demonstrates that geochemical fingerprinting of terrestrial OM should focus on the main lipid sources, rather than the living biomass. Both can exhibit climate-controlled variability, but are generally not identical.

Exact valence bond entanglement entropy and probability distribution in the XXX spin chain and the potts model.

PubMed

Jacobsen, J L; Saleur, H

2008-02-29

We determine exactly the probability distribution of the number N_(c) of valence bonds connecting a subsystem of length L>1 to the rest of the system in the ground state of the XXX antiferromagnetic spin chain. This provides, in particular, the asymptotic behavior of the valence-bond entanglement entropy S_(VB)=N_(c)ln2=4ln2/pi(2)lnL disproving a recent conjecture that this should be related with the von Neumann entropy, and thus equal to 1/3lnL. Our results generalize to the Q-state Potts model.

Constructing a mixed π-conjugated bridge to effectively enhance the nonlinear optical response in the Möbius cyclacene-based systems.

PubMed

Chen, Liwei; Yu, Guangtao; Chen, Wei; Tu, Chunyun; Zhao, Xingang; Huang, Xuri

2014-06-14

Using density functional theory computations, employing the concept of a mixed π-conjugated bridge can effectively improve the first hyperpolarizability (β0) of Möbius cyclacene (MC)-based systems with a D-π-A framework. This mixed π-conjugated bridge is constructed by applying a -(CH=CH)x-NH2 or -(CH=CH)x-NO2 chain to modify [8]MC, which can lead to a considerable β0 value (e.g. [8]MC-(CH=CH)12-NO2 (9.87 × 10(5) au) with only a certain chain length), much larger than the sole [8]MC (261 au) and the corresponding NH2/NO2-modified polyethylene chain with the same π-conjugated length. It is revealed that the substituent sites and the chain length can play a crucial role in improving β0 values of these MC-chain systems, where the β0 value can monotonically increase with increasing -(CH=CH)x- length, and the substituent electron-withdrawing -(CH=CH)x-NO2 chain is superior to the parallel electron-donating -(CH=CH)x-NH2. These appealing findings can provide valuable insights into the design of novel NLO materials based on MC.

Adsorption of poly(ethylene succinate) chain onto graphene nanosheets: A molecular simulation.

PubMed

Kelich, Payam; Asadinezhad, Ahmad

2016-09-01

Understanding the interaction between single polymer chain and graphene nanosheets at local and global length scales is essential for it underlies the mesoscopic properties of polymer nanocomposites. A computational attempt was then performed using atomistic molecular dynamics simulation to gain physical insights into behavior of a model aliphatic polyester, poly(ethylene succinate), single chain near graphene nanosheets, where the effects of the polymer chain length, graphene functionalization, and temperature on conformational properties of the polymer were studied comparatively. Graphene functionalization was carried out through extending the parameters set of an all-atom force field. The results showed a significant conformational transition of the polymer chain from three-dimensional statistical coil, in initial state, to two-dimensional fold, in final state, during adsorption on graphene. The conformational order, overall shape, end-to-end separation statistics, and mobility of the polymer chain were found to be influenced by the graphene functionalization, temperature, and polymer chain length. Furthermore, the polymer chain dynamics mode during adsorption on graphene was observed to transit from normal diffusive to slow subdiffusive mode. The findings from this computational study could shed light on the physics of the early stages of aliphatic polyester chain organization induced by graphene. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural limits on force production and shortening of smooth muscle.

PubMed

Siegman, Marion J; Davidheiser, Sandra; Mooers, Susan U; Butler, Thomas M

2013-02-01

This study determined the factors that limit force production and shortening in two smooth muscles having very different relationships between active and passive force as a function of muscle length. The rat anococcygeus muscle develops active force over the range of lengths 0.2-2.0× the optimum length for force production (Lo). Passive tension due to extension of the resting muscle occurs only at lengths exceeding Lo. In contrast, the rabbit taenia coli develops force in the range of lengths 0.4-1.1 Lo, and passive force which is detectable at 0.56 Lo, increases to ~0.45 maximum active force at Lo, and increases sharply with further extension. The anococcygeus muscle can shorten to 0.2 Lo and the taenia coli to 0.4 Lo. Dynamic stiffness and energy usage at short muscle lengths suggest that the limit of shortening in the taenia coli, in contrast to the anococcygeus muscle, is not due to a failure of cross bridge interaction. Phosphorylation of the regulatory myosin light chains in intact muscles decreased to a small extent at short lengths compared to the decrease in force production. The differences in force production and the extent of shortening in the two muscles was maintained even when, following permeabilization, the myosin light chains were irreversibly phosphorylated with ATPγS, indicating that differences in activation played little, if any role. Ultrastructural studies on resting and activated muscles show that the taenia coli, which is rich in connective tissue (unlike the anococcygeus muscle) undergoes marked cellular twisting and contractile filament misalignment at short lengths with compression of the extracellular matrix. As a result, force is not transmitted in the longitudinal axis of the muscle, but is dissipated against an internal load provided by the compressed extracellular matrix. These observations on two very different normal smooth muscles reveal how differences in the relative contribution of active and passive structural elements determine their mechanical behavior, and how this is potentially modified by remodeling that occurs in disease and in response to changes in functional demand.

Biomimetics of throwing at basketball

NASA Astrophysics Data System (ADS)

Merticaru, E.; Budescu, E.; Iacob, R. M.

2016-08-01

The paper deals with the inverse dynamics of a kinematic chain of the human upper limb when throwing the ball at the basketball, aiming to calculate the torques required to put in action the technical system. The kinematic chain respects the anthropometric features regarding the length and mass of body segments. The kinematic parameters of the motion were determined by measuring the angles of body segments during a succession of filmed pictures of a throw, and the interpolation of these values and determination of the interpolating polynomials for each independent geometric coordinate. Using the Lagrange equations, there were determined the variations with time of the required torques to put in motion the kinematic chain of the type of triple physical pendulum. The obtained values show, naturally, the fact that the biggest torque is that for mimetic articulation of the shoulder, being comparable with those obtained by the brachial biceps muscle of the analyzed human subject. Using the obtained data, there can be conceived the mimetic technical system, of robotic type, with application in sports, so that to perform the motion of ball throwing, from steady position, at the basket.

Synthesis and Crystallization Behavior of Surfactants with Hexamolybdate as the Polar Headgroup

DOE PAGES

Zhu, Li; Chen, Kun; Hao, Jian; ...

2015-06-12

For this paper, alkyl chains with different lengths were covalently grafted onto the surface of hexamolybdate through the postfunctionalization protocol of polyoxometalates. The obtained compounds represent typical structures of the so-called giant surfactants. Unexpectedly, those surfactants with hexamolybdates as polar headgroups are able to crystallize, while single-crystal X-ray diffraction reveals that the crystallization behavior of the surfactants is highly dependent on the length of the alkyl chains. For surfactants with comparatively short alkyl chains (C6 and C10), the alkyl chains prefer to interact with tetrabutylammonium, the countercation of hexamolybdate. However, the alkyl chains tend to pack with each other tomore » form a domain of alkyl chains in the surfactant with a longer alkyl chain (C18). Finally, the possible mechanism is that a long alkyl chain cannot be fully compatible with the short chain (C4) of tetrabutylammonium.« less

Control of in vivo disposition and immunogenicity of polymeric micelles by adjusting poly(sarcosine) chain lengths on surface

NASA Astrophysics Data System (ADS)

Kurihara, Kensuke; Ueda, Motoki; Hara, Isao; Ozeki, Eiichi; Togashi, Kaori; Kimura, Shunsaku

2017-07-01

Four kinds of A3B-type amphiphilic polydepsipeptides, (poly(sarcosine))3- b-poly( l-lactic acid) (the degree of polymerization of poly(sarcosine) are 10, 33, 55, and 85; S10 3 , S33 3 , S55 3 , and S85 3 ) were synthesized to prepare core-shell type polymeric micelles. Their in vivo dispositions and stimulations to trigger immune system to produce IgM upon multiple administrations to mice were examined. With increasing poly(sarcosine) chain lengths, the hydrophilic shell became thicker and the surface density at the most outer surface decreased on the basis of dynamic and static light scattering measurements. These two physical elements of polymeric micelles elicited opposite effects on the immune response in light of the chain length therefore to show an optimized poly(sarcosine) chain length existing between 33mer and 55mer to suppress the accelerated blood clearance phenomenon associated with polymeric micelles.

Chemotaxonomy in some Mediterranean plants and implications for fossil biomarker records

NASA Astrophysics Data System (ADS)

Norström, Elin; Katrantsiotis, Christos; Smittenberg, Rienk H.; Kouli, Katerina

2017-12-01

The increasing utilization of n-alkanes as plant-derived paleo-environmental proxies calls for improved chemotaxonomic control of the modern flora in order to calibrate fossil sediment records to modern analogues. Several recent studies have investigated long-chain n-alkane concentrations and chain-length distributions in species from various vegetation biomes, but up to date, the Mediterranean flora is relatively unexplored in this respect. Here, we analyse the n-alkane concentrations and chain-length distributions in some of the most common species of the modern macchia and phrygana vegetation in south western Peloponnese, Greece. We show that the drought adapted phrygana herbs and shrubs, as well as some of the sclerophyll and gymnosperm macchia components, produce high concentrations of n-alkanes, on average more than double n-alkane production in local wetland reed vegetation. Furthermore, the chain-length distribution in the analysed plants is related to plant functionality, with longer chain lengths associated with higher drought adaptive capacities, probably as a response to long-term evolutionary processes in a moisture limited environment. Furthermore, species with relatively higher average chain lengths (ACL) showed more enriched carbon isotope composition in their tissues (δ13Cplant), suggesting a dual imprint from both physiological and biochemical drought adaptation. The findings have bearings on interpretation of fossil sedimentary biomarker records in the Mediterranean region, which is discussed in relation to a case study from Agios Floros fen, Messenian plain, Peloponnese. The 6000 year long n-alkane record from Agios Floros (ACL, δ13Cwax) is linked to the modern analogue and then evaluated through a comparison with other regional-wide as well as local climate and vegetation proxy-data. The high concentration of long chain n-alkanes in phrygana vegetation suggests a dominating imprint from this vegetation type in sedimentary archives from this ecotone.

Dielectric dispersion for short double-strand DNA.

PubMed

Omori, Shinji; Katsumoto, Yoichi; Yasuda, Akio; Asami, Koji

2006-05-01

A complex dielectric constant for double-strand DNA molecules with a length of not greater than 120 base pairs in an aqueous solution containing 30 mM NaCl was systematically measured as a function of chain length in such a way that experimental uncertainties associated with the molecular-weight distribution of specimens were virtually excluded. In contrast to the past experimental and theoretical studies for much longer DNA molecules, both the molar specific dielectric increment and the relaxation time are proportional to the chain length. These scaling rules cannot be accounted for by any theory so far proposed that gives analytical expressions for those two quantities in the long-chain limit.

Influence of chlorine atoms in bay positions of perylene-tetracarboxylic acids on their spectral properties in Langmuir-Blodgett films

NASA Astrophysics Data System (ADS)

Piosik, Emilia; Synak, Anna; Martyński, Tomasz

2018-01-01

The influence of chlorine atoms in the bay positions of the perylene-3,4,9,10-tetracarboxylic acids with the different alkyl chains length on their spectral properties in monomolecular films has been studied. The chlorinated (PCln) and for comparison non-chlorinated (Pn) perylene derivatives were deposited onto quartz plates using a Langmuir-Blodgett (LB) technique. The absorption spectra showed that the PCln and Pn dyes form in monolayers the I- and J-type aggregates, respectively. In turn, their steady-state and time-resolved emission spectra revealed presence of two emitter types, which we assigned to monomers and excimers. The luminescence lifetimes of the PCln monomers and excimers determined with a time-correlated single photon counting method (TCSPC) are significantly shorter than these obtained for the same emitter types in the Pn monolayers. In the case of the chlorinated dyes, the contribution of the monomer emission dominates over the excimer emission and is almost independent from the alkyl chain length. By contrast, the share of the Pn monomer emission increases strongly with a number of carbon atoms in their hydrocarbon chains. The luminescence quantum yields (LQY) of the Pn and PCln monolayers measured in an integrating sphere are in the range of 0.06-0.11. The presented results reveal that the PCln dyes exhibit lower tendency for aggregation than the non-chlorinated derivatives. It can be explained by limited intermolecular interaction between neighbouring PCln molecules caused by deformation of the perylene core as a result of strongly electronegative chlorine atoms in the bay positions of these dyes. Moreover, the strong influence of the alkyl chain length on the Pn aggregation contrary to the case of the PCln derivatives was observed.

ELISA assays and alcohol: increasing carbon chain length can interfere with detection of cytokines

PubMed Central

von Maltzan, Kristine; Pruett, Stephen B.

2010-01-01

Enzyme-linked immunosorbent assays (ELISA) are frequently used in studies on cytokine production in response to treatment of cell cultures or laboratory animals. When an ELISA assay is performed on cell culture supernatants, samples often contain the treatment agents. The purpose of the present study was to determine if some of the agents evaluated might inhibit cytokine detection by interfering with the ELISA, leaving the question of whether cytokine production was inhibited unanswered. Mouse and human cytokine ELISA kits from BD Biosciences were used according to the manufacturer’s instructions. Cytokine proteins were subjected to one to five carbon alcohols at 86.8 mM (methanol, ethanol, 1-propanol, 2-propanol, n-butanol, and n-pentanol). After treating cell cultures with alcohols of different carbon chain lengths, we found that some of the alcohols interfered with measurement of some cytokines by ELISA, thus making their effects on cytokine production by cells in culture unclear. Increasing carbon chain length of straight chain alcohols positively correlated with their ability to inhibit detection of TNF-α and IL-10, but not with the detection of IL-6, IL-8, and IL-12. To avoid misinterpretation of treatment effects, ELISA assays should be tested with the reference protein and the treatment agent first, before testing biological samples. These results along with other recent results we obtained using circular dichroism indicate that alcohols with 2 or more carbons can directly alter protein conformation enough to disrupt binding in an ELISA (shown in the present study) or to inhibit ligand induced conformational changes (results not shown). Such direct effects have not been given enough consideration as a mechanism of ethanol action in the immune system. PMID:20843633

Controlling the size of hot injection made nanocrystals by manipulating the diffusion coefficient of the solute.

PubMed

De Nolf, Kim; Capek, Richard K; Abe, Sofie; Sluydts, Michael; Jang, Youngjin; Martins, José C; Cottenier, Stefaan; Lifshitz, Efrat; Hens, Zeger

2015-02-25

We investigate the relation between the chain length of ligands used and the size of the nanocrystals formed in the hot injection synthesis. With two different CdSe nanocrystal syntheses, we consistently find that longer chain carboxylic acids result in smaller nanocrystals with improved size dispersions. By combining a more in-depth experimental investigation with kinetic reaction simulations, we come to the conclusion that this size tuning is due to a change in the diffusion coefficient and the solubility of the solute. The relation between size tuning by the ligand chain length and the coordination of the solute by the ligands is further explored by expanding the study to amines and phosphine oxides. In line with the weak coordination of CdSe nanocrystals by amines, no influence of the chain length on the nanocrystals is found, whereas the size tuning brought about by phosphine oxides can be attributed to a solubility change. We conclude that the ligand chain length provides a practical handle to optimize the outcome of a hot injection synthesis in terms of size and size dispersion and can be used to probe the interaction between ligands and the actual solute.

Self-assembly assisted polymerization (SAAP): approaching long multi-block copolymers with an ordered chain sequence and controllable block length.

PubMed

Wu, Chi; Xie, Zuowei; Zhang, Guangzhao; Zi, Guofu; Tu, Yingfeng; Yang, Yali; Cai, Ping; Nie, Ting

2002-12-07

A combination of polymer physics and synthetic chemistry has enabled us to develop self-assembly assisted polymerization (SAAP), leading to the preparation of long multi-block copolymers with an ordered chain sequence and controllable block lengths.

Effect of chain stiffness on the competition between crystallization and glass-formation in model unentangled polymers

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Smith, Tyler B.; Hoy, Robert S.; Karayiannis, Nikos Ch.

2015-10-01

We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of chain stiffness, spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter (lK/r0) increases monotonically with increasing bending stiffness kb and yields a one-parameter model that relates chain shape to bulk morphology. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order. In the rodlike limit, nematic chain ordering typical of lamellar precursors coexists with close-packing. At intermediate values of bending stiffness, the competition between random-walk-like and nematic chain ordering produces glass-formation; the range of kb over which this occurs increases with the thermal cooling rate | T ˙ | implemented in our molecular dynamics simulations. Finally, values of kb between the glass-forming and rodlike ranges produce complex ordered phases such as close-packed spirals. Our results should provide a useful initial step in a coarse-grained modeling approach to systematically determining the effect of chain stiffness on the crystallization-vs-glass-formation competition in both synthetic and colloidal polymers.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

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

PubMed

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

2015-07-07

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

Atomistic Simulations of Hydrodynamic and Interaction Forces on Functionalized Silica Nanoparticles

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Ismail, Ahmed E.; Chandross, Michael; Lorenz, Christian D.; Grest, Gary S.

2009-03-01

It is often desired to prevent the flocculation and phase separation of nanoparticles in solution. This can be accomplished either by manipulating the solvent or by tailoring the surface chemistry of the nanoparticles through functionalization with a monolayer of oligomer chains. Since it is not known how these functionalized coatings affect the interactions between nanoparticles and with the surrounding solvent, we present results from a series of molecular dynamics simulations of polyethylene oxide (PEO) coated silica nanoparticles of varying size (5 to 20 nm diameter) in water. For a single nanoparticle we determined the Stokes drag on the nanoparticle as it moves through the solvent and as it approaches a wall. Due to hydrodynamic interactions there are large finite size effects which we estimate by varying the size of the simulation cell. We also determined both solvent-mediated (velocity-independent) and lubrication (velocity-dependent) forces between two nanoparticles as a function of the coverage and chain length of the PEO chains.

Triazolium based ionic liquid crystals: Effect of asymmetric substitution

DOE PAGES

Stappert, K.; Mudring, A. -V.

2015-01-27

A new series of ten different asymmetrical 1-dodecyl-3-alkyl-triazolium bromides, [C 12C nTr][Br], has been synthesized and their mesomorphic behavior studied by DSC (differential scanning calorimetry), POM (polarizing optical microscopy) and SAXS (small angle X-ray scattering). The influence of the chain length of the triazolium salts is investigated to explore the effect of asymmetric substitution on the phase behaviour of these compounds. For that reason, the length of one alkyl chain was varied from 14 to 1 carbon atoms (n = 14, 12, 10, 8–4, 2, 1) while the other alkyl chain was kept at 12 carbon. Single crystal X-ray structuremore » analysis of compounds [C 12C 12Tr][Br] and [C 12C 5Tr][Br] reveal that the cations adopt a U-shaped conformation with head-to-head arranged triazolium cores. In contrast, for [C 12C 1Tr][Br], a rod like shape of the cation with interdigitated alkyl chains is found. All investigated compounds are thermotropic liquid crystals. Higher ordered smectic phases, smectic C as well as smectic A phases were found depending on the chain length of the cation. Moreover, the clearing point temperature decreases with decreasing chain length with exception for the n-dodecyl-3-alkyltrizoliumbromides with the two shortest alkyl chains, [C 12C 2Tr][Br] and [C 12C 1Tr][Br], which present higher clearing temperatures (86 and 156 °C) and are structurally distinctly different.« less

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length

PubMed Central

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S.; Du, Yang; Nielsen, Anne K.; Byrne, Bernadette; Kobilka, Brian K.; Loland, Claus J.; Guan, Lan

2017-01-01

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile–lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. PMID:27981750

Forced reptation revealed by chain pull-out simulations.

PubMed

Bulacu, Monica; van der Giessen, Erik

2009-08-14

We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based on the Kremer-Grest model, extended to account for stiffness along the chain backbone. Forced reptation of the connectors was observed during their disentanglement from the bulk chains. The extracted chains are clearly seen following an imaginary "tube" inside the bulks as they are pulled out. The entropic and energetic responses to the external deformation are investigated by monitoring the connector conformation tensor and the modifications of the internal parameters (bonds, bending, and torsion angles along the connectors). The work needed to separate the two bulks is computed from the tensile force induced during debonding in the connector chains. The value of the work reached at total separation is considered as the debonding energy G. The most important parameters controlling G are the length (n) of the chains placed at the interface and their areal density. Our in silico experiments are performed at relatively low areal density and are disregarded if chain scission occurs during disentanglement. As predicted by the reptation theory, for this pure pull-out regime, the power exponent from the scaling G proportional, variant n(a) is a approximately 2, irrespective of chain stiffness. Small variations are found when the connectors form different number of stitches at the interface, or when their length is randomly distributed in between the two bulks. Our results show that the effects of the number of stitches and of the randomness of the block lengths have to be considered together, especially when comparing with experiments where they cannot be controlled rigorously. These results may be significant for industrial applications, such reinforcement of polymer-polymer adhesion by connector chains, when incorporated as constitutive laws at higher time/length scales in finite element calculations.

Direct quantification of molar masses of copolymers by online liquid chromatography under critical conditions-nuclear magnetic resonance and size exclusion chromatography-nuclear magnetic resonance.

PubMed

Hehn, Mathias; Wagner, Thomas; Hiller, Wolf

2014-01-07

Online LCCC-NMR and SEC-NMR are compared regarding the determination of molar masses of block copolymers. Two different direct referencing methods are particularly demonstrated in LCCC-NMR for a detailed characterization of diblock copolymers and their co-monomers. First, an intramolecular reference group was used for the direct determination of block lengths and molar masses. For the first time, it was shown that LCCC-NMR can be used for an accurate determination of Mw and Mn of copolymers. These data were in perfect agreement with SEC-NMR measurements using the same intramolecular referencing method. In contrast, the determination of molar masses with common relative methods based on calibrations with homopolymers delivered inaccurate results for all investigated diblock copolymers due to different hydrodynamic volumes of the diblock copolymer compared to their homopolymers. The intramolecular referencing method provided detailed insights in the co-monomer behavior during the chromatographic separation of LCCC. Especially, accurate chain lengths and chemical compositions of the "invisible" and "visible" blocks were quantified during the elution under critical conditions and provided new aspects to the concept of critical conditions. Second, an external reference NMR signal was used to directly determine concentrations and molar masses of the block copolymers from the chromatographic elution profile. Consequently, the intensity axes of the resulting chromatograms were converted to molar amounts and masses, allowing for determination of the amount of polymer chains with respect to elution volume, the evaluation of the limiting magnitude of concentration for LCCC-NMR, and determination of the molar masses of copolymers.

Determination of the thermal stability of perfluoropolyalkyl ethers by tensimetry

NASA Technical Reports Server (NTRS)

Helmick, Larry A.; Jones, William R., Jr.

1992-01-01

The thermal decomposition temperatures of several perfluoropolyalkyl ether fluids were determined with a computerized tensimeter. In general, the decomposition temperatures of the commercial fluids were all similar and significantly higher than those for noncommercial fluids. Correlation of the decomposition temperatures with the molecular structures of the primary components of the commercial fluids revealed that the stability of the fluids was not affected by carbon chain length, branching, or adjacent difluoroformal groups. Instead, stability was limited by the presence of small quantities of thermally unstable material and/or chlorine-containing material arising from the use of chlorine containing solvents during synthesis. Finally, correlation of decomposition temperatures with molecular weights for two fluids supports a chain cleavage reaction mechanism for one and an unzipping reaction mechanism for the other.

Persistence length changes dramatically as RNA folds.

PubMed

Caliskan, G; Hyeon, C; Perez-Salas, U; Briber, R M; Woodson, S A; Thirumalai, D

2005-12-31

We determine the persistence length l(p) for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P(r) obtained from small angle x-ray scattering intensity data to the asymptotic form of the calculated P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length.

Effects of alkyl chain length and substituent pattern of fullerene bis-adducts on film structures and photovoltaic properties of bulk heterojunction solar cells.

PubMed

Tao, Ran; Umeyama, Tomokazu; Kurotobi, Kei; Imahori, Hiroshi

2014-10-08

A series of alkoxycarbonyl-substituted dihydronaphthyl-based [60]fullerene bis-adduct derivatives (denoted as C2BA, C4BA, and C6BA with the alkyl chain of ethyl, n-butyl, and n-hexyl, respectively) have been synthesized to investigate the effects of alkyl chain length and substituent pattern of fullerene bis-adducts on the film structures and photovoltaic properties of bulk heterojunction polymer solar cells. The shorter alkyl chain length caused lower solubility of the fullerene bis-adducts (C6BA > C4BA > C2BA), thereby resulting in the increased separation difficulty of respective bis-adduct isomers. The device performance based on poly(3-hexylthiophene) (P3HT) and the fullerene bis-adduct regioisomer mixtures was enhanced by shortening the alkyl chain length. When using the regioisomerically separated fullerene bis-adducts, the devices based on trans-2 and a mixture of trans-4 and e of C4BA exhibited the highest power conversion efficiencies of ca. 2.4%, which are considerably higher than those of the C6BA counterparts (ca. 1.4%) and the C4BA regioisomer mixture (1.10%). The film morphologies as well as electron mobilities of the P3HT:bis-adduct blend films were found to affect the photovoltaic properties considerably. These results reveal that the alkyl chain length and substituent pattern of fullerene bis-adducts significantly influence the photovoltaic properties as well as the film structures of bulk heterojunction solar cells.

Thermal conductivity of the Lennard-Jones chain fluid model.

PubMed

Galliero, Guillaume; Boned, Christian

2009-12-01

Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8

Chain Dynamics in a Dilute Magnetorheological Fluid

NASA Technical Reports Server (NTRS)

Liu, Jing; Hagenbuchle, Martin

1996-01-01

The structure, formation, and dynamics of dilute, mono-dispersive ferrofluid emulsions in an external magnetic field have been investigated using dynamic light scattering techniques. In the absence of the magnetic field, the emulsion particles are randomly distributed and behave like hard spheres in Brownian motion. An applied magnetic field induces a magnetic dipole moment in each particle. Dipolar interactions between particles align them into chains where correlation functions show two decay processes. The short-time decay shows the motion of straight chains as a whole where the apparent chain length increases with the applied magnetic field and the particle volume fraction. Good scaling results are obtained showing that the apparent chain length grows with time following a power law with exponent of 0.6 and depends on the applied field, particle volume fraction, and diffusion constant of the particles. The long-time decay in the correlation function shows oscillation when the chains reach a certain length with time and stiffness with threshold field This result shows that chains not only fluctuate, but move in a periodic motion with a frequency of 364 Hz at lambda = 15. It may suggest the existence of phonons. This work is the first step in the understanding of the structure formation, especially chain coarsening mechanism, of magnetorheological (MR) fluids at higher volume fractions.

Costs of logging thinnings and a clearcutting in Appalachia using a truck-mounted crane

Treesearch

Raymond L. Sarles; Kenneth R. Whitenack

1984-01-01

Four timber cutting treatments - three levels of thinning and a clearcutting - were applied on 60-year-old mountain stands of Allegheny hardwoods. The stands were logged by a three-man crew using chain saws and a truck-mounted crane. Logging operations were studied, and production rates determined for tree-length logs decked at roadside. Work efficiency and...

Modification of eucalyptus pulp fiber using silane coupling agents with aliphatic side chains of different length

USDA-ARS?s Scientific Manuscript database

The objective of this work was to evaluate the effect of three silane coupling agents with different aliphatic chain lengths on the hydrophobicity of eucalyptus pulp fiber. The three silanes coupling agents used (isobutyltrimethoxysilane, methyltrimethoxysilane, and n-octyltriethoxysilane [OTES]) we...

Impact of Polymer Electrolyte Membrane Degradation Products on Oxygen Reduction Reaction Activity for Platinum Electrocatalysts

DOE PAGES

Christ, J. M.; Neyerlin, K. C.; Wang, H.; ...

2014-10-30

The impact of model membrane degradation compounds on the relevant electrochemical parameters for the oxygen reduction reaction (i.e. electrochemical surface area and catalytic activity), was studied for both polycrystalline Pt and carbon supported Pt electrocatalysts. Model compounds, representing previously published, experimentally determined polymer electrolyte membrane degradation products, were in the form of perfluorinated organic acids that contained combinations of carboxylic and/or sulfonic acid functionality. Perfluorinated carboxylic acids of carbon chain length C1 – C6 were found to have an impact on electrochemical surface area (ECA). The longest chain length acid also hindered the observed oxygen reduction reaction (ORR) performance, resultingmore » in a 17% loss in kinetic current (determined at 0.9 V). Model compounds containing sulfonic acid functional groups alone did not show an effect on Pt ECA or ORR activity. Lastly, greater than a 44% loss in ORR activity at 0.9V was observed for diacid model compounds DA-Naf (perfluoro(2-methyl-3-oxa-5-sulfonic pentanoic) acid) and DA-3M (perfluoro(4-sulfonic butanoic) acid), which contained both sulfonic and carboxylic acid functionalities.« less

Molecular dynamics simulation of the folding of single alkane chains with different lengths on single-walled carbon nanotubes and graphene.

PubMed

Liu, Yan Fang; Yang, Hua; Zhang, Hui

2018-05-31

Chain folding is an important step during polymer crystallization. In order to study the effects of the surface on chain folding, molecular dynamics simulations of the folding of different alkane chains on three kinds of single-walled carbon nanotubes (SWCNTs) and graphene were performed. The folding behaviors of the single alkane chains on these surfaces were found to be different from their folding behaviors in vacuum. The end-to-end distances of the chains were calculated to explore the chain folding. An increasing tendency to fold into two or more stems with increasing alkane chain length was observed. This result indicates that the occurrence and the stability of chain folding are related to the surface curvature, the diameter of the SWCNT, and surface texture. In addition, the angle between the direction of the alkane chain segment and the direction of the surface texture was measured on different surfaces.

Quantum discord length is enhanced while entanglement length is not by introducing disorder in a spin chain.

PubMed

Sadhukhan, Debasis; Roy, Sudipto Singha; Rakshit, Debraj; Prabhu, R; Sen De, Aditi; Sen, Ujjwal

2016-01-01

Classical correlation functions of ground states typically decay exponentially and polynomially, respectively, for gapped and gapless short-range quantum spin systems. In such systems, entanglement decays exponentially even at the quantum critical points. However, quantum discord, an information-theoretic quantum correlation measure, survives long lattice distances. We investigate the effects of quenched disorder on quantum correlation lengths of quenched averaged entanglement and quantum discord, in the anisotropic XY and XYZ spin glass and random field chains. We find that there is virtually neither reduction nor enhancement in entanglement length while quantum discord length increases significantly with the introduction of the quenched disorder.

A jojoba beta-Ketoacyl-CoA synthase cDNA complements the canola fatty acid elongation mutation in transgenic plants.

PubMed Central

Lassner, M W; Lardizabal, K; Metz, J G

1996-01-01

beta-Ketoacyl-coenzyme A (CoA) synthase (KCS) catalyzes the condensation of malonyl-CoA with long-chain acyl-CoA. This reaction is the initial step of the microsomal fatty acyl-CoA elongation pathway responsible for formation of very long chain fatty acids (VLCFAs, or fatty acids with chain lengths > 18 carbons). Manipulation of this pathway is significant for agriculture, because it is the basis of conversion of high erucic acid rapeseed into canola. High erucic acid rapeseed oil, used as an industrial feedstock, is rich in VLCFAs, whereas the edible oil extracted from canola is essentially devoid of VLCFAs. Here, we report the cloning of a cDNA from developing jojoba embryos involved in microsomal fatty acid elongation. The jojoba cDNA is homologous to the recently cloned Arabidopsis FATTY ACID ELONGATION1 (FAE1) gene that has been suggested to encode KCS. We characterize the jojoba enzyme and present biochemical data indicating that the jojoba cDNA does indeed encode KCS. Transformation of low erucic acid rapeseed with the jojoba cDNA restored KCS activity to developing embryos and altered the transgenic seed oil composition to contain high levels of VLCFAs. The data reveal the key role KCS plays in determining the chain lengths of fatty acids found in seed oils. PMID:8742713

A jojoba beta-Ketoacyl-CoA synthase cDNA complements the canola fatty acid elongation mutation in transgenic plants.

PubMed

Lassner, M W; Lardizabal, K; Metz, J G

1996-02-01

beta-Ketoacyl-coenzyme A (CoA) synthase (KCS) catalyzes the condensation of malonyl-CoA with long-chain acyl-CoA. This reaction is the initial step of the microsomal fatty acyl-CoA elongation pathway responsible for formation of very long chain fatty acids (VLCFAs, or fatty acids with chain lengths > 18 carbons). Manipulation of this pathway is significant for agriculture, because it is the basis of conversion of high erucic acid rapeseed into canola. High erucic acid rapeseed oil, used as an industrial feedstock, is rich in VLCFAs, whereas the edible oil extracted from canola is essentially devoid of VLCFAs. Here, we report the cloning of a cDNA from developing jojoba embryos involved in microsomal fatty acid elongation. The jojoba cDNA is homologous to the recently cloned Arabidopsis FATTY ACID ELONGATION1 (FAE1) gene that has been suggested to encode KCS. We characterize the jojoba enzyme and present biochemical data indicating that the jojoba cDNA does indeed encode KCS. Transformation of low erucic acid rapeseed with the jojoba cDNA restored KCS activity to developing embryos and altered the transgenic seed oil composition to contain high levels of VLCFAs. The data reveal the key role KCS plays in determining the chain lengths of fatty acids found in seed oils.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

PubMed

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Radiolysis of N-acetyl amino acids as model compounds for radiation degradation of polypeptides

NASA Astrophysics Data System (ADS)

Wayne Garrett, R.; Hill, David J. T.; Ho, Sook-Ying; O'Donnell, James H.; O'Sullivan, Paul W.; Pomery, Peter J.

Radiation chemical yields of (i) the volatile radiolysis products and (ii) the trapped free radicals from the y-radiolysis of the N-acetyl derivatives of glycine, L-valine, L-phenylalanine and L-tyrosine in the polycrystalline state have been determined at room temperature (303 K). Carbon dioxide was found to be the major molecular product for all these compounds with G(CO 2) varying from 0.36 for N-acetyl-L-tyrosine to 8 for N-acetyl-L-valine. There was evidence for some scission of the N-C α bond, indicated by the production of acetamide and the corresponding aliphatic acid, but the determination reaction was found to be of much lesser importance than the decarboxylation reaction. A protective effect of the aromatic ring in N-acetyl-L-phenylalanine and in N-acetyl-L-tyrosine was indicated by the lower yields of volatile products for these compounds. The yields of trapped free radicals were found to vary with the nature of the amino acid side chain, increasing with chain length and chain branching. The radical yields were decreased by incorporation of an aromatic moiety in the side chain, this effect being greater for the tyrosyl side chain than for the phenyl side chain. The G(R·) values showed a good correlation with G(CO 2) indicating that a common reaction may be involved in radical production and carbon dioxide formation.

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

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

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomicmore » spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.« less

Physico-Chemical Properties and Phase Behaviour of Pyrrolidinium-Based Ionic Liquids

PubMed Central

Domańska, Urszula

2010-01-01

A review of the relevant literature on 1-alkyl-1-methylpyrrolidinium-based ionic liquids has been presented. The phase diagrams for the binary systems of {1-ethyl-1-methylpyrrolidinium trifluoromethanesulfonate (triflate) [EMPYR][CF3SO3] + water, or + 1-butanol} and for the binary systems of {1-propyl-1-methylpyrrolidinium trifluoromethanesulfonate (triflate) [PMPYR][CF3SO3] + water, or + an alcohol (1-butanol, 1-hexanol, 1-octanol, 1-decanol)} have been determined at atmospheric pressure using a dynamic method. The influence of alcohol chain length was discussed for the [PMPYR][CF3SO3]. A systematic decrease in the solubility was observed with an increase of the alkyl chain length of an alcohol. (Solid + liquid) phase equilibria with complete miscibility in the liquid phase region were observed for the systems involving water and alcohols. The solubility of the ionic liquid increases as the alkyl chain length on the pyrrolidinium cation increases. The correlation of the experimental data has been carried out using the Wilson, UNIQUAC and the NRTL equations. The phase diagrams reported here have been compared to the systems published earlier with the 1-alkyl-1-methylpyrrolidinium-based ionic liquids. The influence of the cation and anion on the phase behaviour has been discussed. The basic thermal properties of pure ILs, i.e., melting temperature and the enthalpy of fusion, the solid-solid phase transition temperature and enthalpy have been measured using a differential scanning microcalorimetry technique. PMID:20480044

Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers.

PubMed Central

Marchal, D; Boireau, W; Laval, J M; Moiroux, J; Bourdillon, C

1998-01-01

The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ10 or PQ9 was 2.0 +/- 0.4 x 10(-8) cm2 s(-1) at 30 degrees C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4-13 pH range. For a series of isoprenoid quinones, UQ2 or PQ2 to UQ10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer. PMID:9545054

Anti-Caries Effects of Dental Adhesives Containing Quaternary Ammonium Methacrylates with Different Chain Lengths

PubMed Central

Han, Qi; Li, Bolei; Zhou, Xuedong; Ge, Yang; Wang, Suping; Li, Mingyun; Ren, Biao; Wang, Haohao; Zhang, Keke; Xu, Hockin H. K.; Peng, Xian; Feng, Mingye; Weir, Michael D.; Chen, Yu; Cheng, Lei

2017-01-01

The objectives of this study were to investigate the effects of dental adhesives containing quaternary ammonium methacrylates (QAMs) with different alkyl chain lengths (CL) on ecological caries prevention in vitro. Five QAMs were synthesized with a CL = 3, 6, 9, 12, and 16 and incorporated into adhesives. Micro-tensile bond strength and surface charge density were used to measure the physical properties of the adhesives. The proportion change in three-species biofilms consisting of Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii was tested using the TaqMan real-time polymerase chain reaction. Lactic acid assay, MTT [3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, exopolysaccharide staining, live/dead staining, scanning electron microscopy (SEM), and transverse microradiography (TMR) were performed to study the anti-biofilm and anti-demineralization effects of the dental adhesives. The results showed that incorporating QAMs with different alkyl chain lengths into the adhesives had no obvious effect on the dentin bond strength. The adhesives containing QAMs with a longer alkyl chain developed healthier biofilms. The surface charge density, anti-biofilm, and anti-demineralization effects of the adhesives increased with a CL of the QAMs from 3 to 12, but decreased slightly with a CL from 12 to 16. In conclusion, adhesives containing QAMs with a tailored chain length are promising for preventing secondary caries in an “ecological way”. PMID:28773004

Application of small-angle neutron scattering to the study of forces between magnetically chained monodisperse ferrofluid emulsion droplets

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

Jain, Dr Nirmesh; Liu, Dr C K; Hawkett, Dr B. S.

2014-01-01

The optical magnetic chaining technique (MCT) developed by Leal-Calderon, Bibette and co-workers in the 1990 s allows precise measurements of force profiles between droplets in monodisperse ferrofluid emulsions. However, the method lacks an in-situ determination of droplet size and therefore requires the combination of separately acquired measurements of droplet chain periodicity versus an applied magnetic field from optical Bragg scattering and droplet diameter inferred from dynamic light scattering (DLS) to recover surface force-distance profiles between the colloidal particles. Compound refractive lens (CRL) focussed small-angle scattering (SANS) MCT should result in more consistent measurements of droplet size (form factor measurements inmore » the absence of field) and droplet chaining period (from structure factor peaks when the magnetic field is applied); and, with access to shorter length scales, extend force measurements to closer approaches than possible by optical measurements. We report on CRL-SANS measurements of monodisperse ferrofluid emulsion droplets aligned in straight chains by an applied field perpendicular to the incident beam direction. Analysis of the scattering from the closely spaced droplets required algorithms that carefully treated resolution and its effect on mean scattering vector magnitudes in order to determine droplet size and chain periods to sufficient accuracy. At lower applied fields scattering patterns indicate structural correlations transverse to the magnetic field direction due to the formation of intermediate structures in early chain growth.« less

On the theory of hysteretic magnetostriction of soft ferrogels

NASA Astrophysics Data System (ADS)

Zubarev, Andrey; Chirikov, Dmitry; Stepanov, Gennady; Borin, Dmitry; Lopez-Lopez, M. T.

2018-05-01

The paper deals with theoretical study of hysteretic magnetostriction of soft ferrogels - composite materials, consisting of the micron-sized magnetizable particles embedded into gel matrices. It is supposed that initially, before application of an external magnetic field, the particles are homogeneously and isotropically distributed in an elastic matrix. The theoretical explanation of the hysteresis phenomena is based on the conception that, under the field action, the particles rearrange into the linear chain-like aggregates. The typical length of the chains is determined by the competition between the force of magnetic attraction of the particles and the force of elastic deformation of the matrix.

29 CFR 1915.112 - Ropes, chains and slings.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., defective welds, deformation and increase in length or stretch. (3) Employers must note interlink wear, not accompanied by stretch in excess of 5 percent, and remove the chain from service when maximum allowable wear... shall be removed from service when, due to stretch, the increase in length of a measured section exceeds...

29 CFR 1915.112 - Ropes, chains and slings.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., defective welds, deformation and increase in length or stretch. (3) Employers must note interlink wear, not accompanied by stretch in excess of 5 percent, and remove the chain from service when maximum allowable wear... shall be removed from service when, due to stretch, the increase in length of a measured section exceeds...

29 CFR 1915.112 - Ropes, chains and slings.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., defective welds, deformation and increase in length or stretch. (3) Employers must note interlink wear, not accompanied by stretch in excess of 5 percent, and remove the chain from service when maximum allowable wear... shall be removed from service when, due to stretch, the increase in length of a measured section exceeds...

pi-Selective stationary phases: (II) Adsorption behavior of substituted aromatic compounds on n-alkyl-phenyl stationary phases

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

Gritti, Fabrice; Guiochon, Georges A; Mayfield, Kirsty

2010-01-01

The frontal analysis method was used to measure the adsorption isotherms of phenol, 4-chlorophenol, p-cresol, 4-methoxyphenol and caffeine on a series of columns packed with home-made alkyl-phenyl bonded silica particles. These ligands consist of a phenyl ring tethered to the silica support via a carbon chain of length ranging from 0 to 4 atoms. The adsorption isotherm models that fit best to the data account for solute-solute interactions that are likely caused by p-p interactions occurring between aromatic compounds and the phenyl group of the ligand. These interactions are the dominant factor responsible for the separation of low molecular weightmore » aromatic compounds on these phenyl-type stationary phases. The saturation capacities depend on whether the spacer of the ligands have an even or an odd number of carbon atoms, with the even alkyl chain lengths having a greater saturation capacity than the odd alkyl chain lengths. The trends in the adsorption equilibrium constant are also significantly different for the even and the odd chain length ligands.« less

Gel Permeation Chromatography Characterization of the Chain Length Distributions in Thiol-Acrylate Photopolymer Networks

PubMed Central

Rydholm, Amber E.; Held, Nicole L.; Bowman, Christopher N.; Anseth, Kristi S.

2008-01-01

Crosslinked, degradable networks formed from the photopolymerization of thiol and acrylate monomers are explored as potential biomaterials. The degradation behavior and material properties of these networks are influenced by the molecular weight of the nondegradable thiol-polyacrylate backbone chains that form during photopolymerization. Here, gel permeation chromatography was used to characterize the thiol-polyacrylate backbone chain lengths in degraded thiol-acrylate networks. Increasing thiol functionality from 1 to 4 increased the backbone molecular weight (M̄w = 2.3 ± 0.07 × 104 Da for monothiol and 3.6 ± 0.1 × 104 Da for tetrathiol networks). Decreasing thiol functional group concentration from 30 to 10 mol% also increased the backbone lengths (M̄w = 7.3 ± 1.1 × 104 Da for the networks containing 10 mol% thiol groups as compared to 3.6 ± 0.1 × 104 Da for 30 mol% thiol). Finally, the backbone chain lengths were probed at various stages of degradation and an increase in backbone molecular weight was observed as mass loss progressed from 10 to 70%. PMID:19079733

First-flush loads of perfluorinated compounds in stormwater runoff from Hayabuchi River basin, Japan served by separated sewerage system.

PubMed

Zushi, Yasuyuki; Masunaga, Shigeki

2009-08-01

Worldwide environmental pollution by perfluorinated compounds (PFCs) has been reported. PFCs have also been reported to have nonpoint sources (NPSs). A fixed-point hourly monitoring in the river was conducted during a storm event using an automatic sampler to estimate the impact of the first-flush of PFCs from NPS in this study. Perfluorocarboxylates (PFCAs) and perfluoroalkyl sulfonates (PFASs) with different chain lengths were monitored. The concentrations of short- to medium-chain-length PFCAs such as PFHpA, PFOA and PFNA, and PFASs such as PFBS, PFPeS, PFHxS, PFHpS and PFOS showed no marked increase with the storm-runoff event. However, in contrast to this, concentrations of long-chain-length PFCAs such as PFDA and PFUnA increased markedly. The concentrations of PFDA and PFUnA increased 3.4 (1.5-5.0 ng L(-1))- and 2.0 (3.3-6.7 ng L(-1))-fold, respectively. This study demonstrates that large loads of long-chain-length PFCAs are discharged to the Hayabuchi River during the first-flush after the rain event.

How a Small Quantum Bath Can Thermalize Long Localized Chains

NASA Astrophysics Data System (ADS)

Luitz, David J.; Huveneers, François; De Roeck, Wojciech

2017-10-01

We investigate the stability of the many-body localized phase for a system in contact with a single ergodic grain modeling a Griffiths region with low disorder. Our numerical analysis provides evidence that even a small ergodic grain consisting of only three qubits can delocalize a localized chain as soon as the localization length exceeds a critical value separating localized and extended regimes of the whole system. We present a simple theory, consistent with De Roeck and Huveneers's arguments in [Phys. Rev. B 95, 155129 (2017), 10.1103/PhysRevB.95.155129] that assumes a system to be locally ergodic unless the local relaxation time determined by Fermi's golden rule is larger than the inverse level spacing. This theory predicts a critical value for the localization length that is perfectly consistent with our numerical calculations. We analyze in detail the behavior of local operators inside and outside the ergodic grain and find excellent agreement of numerics and theory.

Binding of alkylphenols and alkylated non-phenolics to the rainbow trout (Oncorhynchus mykiss) plasma sex steroid-binding protein.

PubMed

Tollefsen, K-E

2007-09-01

Alkylphenols are well-known endocrine disrupters, mediating effects through the estrogen receptor (ER). Although the estrogenic properties of the alkylphenols are well documented, alternative mechanisms of action are poorly described. In the present work, the interaction of a range of alkyl-substituted phenols and alkyl-substituted non-phenolics with the rainbow trout (Oncorhynchus mykiss) sex steroid-binding protein (rtSBP) were determined by competitive ligand-binding studies. The role of alkyl chain length and branching, substituent position, number of alkylated groups, and the requirement of a phenolic ring structure were assessed. The results showed that the rtSBP binds to most chemical structures tested, although the highest affinity was obtained for mono-substituted alkylphenols with a chain length of four to eight methyl groups. Interestingly, rtSBP binding was also observed for non-phenolic compounds such as 4-t-butylcyclohexanol and 4-t-butylnitrobenzene suggesting that the rtSBP has a broad binding specificity for alkylphenols and alkylated non-phenolics.

Binding of alkylphenols and alkylated non-phenolics to rainbow trout (Oncorhynchus mykiss) hepatic estrogen receptors.

PubMed

Tollefsen, Knut-Erik; Julie Nilsen, Anja

2008-02-01

Alkylphenols are well-known endocrine disrupters, mediating effects through the estrogen receptor (ER). In the present work, the interaction of alkylphenols and alkylated non-phenolics with hepatic rainbow trout (Oncorhynchus mykiss) estrogen receptors (rtERs) was determined. The role of alkyl chain length and branching, substituent position, number of alkylated groups, and the requirement of a phenolic ring structure was assessed. The results showed that the rtERs bound most alkylphenols, although with 20,000 to 2 million times lower affinity than the endogenous estrogen 17beta-estradiol. Mono-substituted alkylphenols with moderate (C4-C6) and long (C8 and C12) alkyl chain length in the para position exhibited the highest affinity for the rtERs. Substitution with multiple alkyl groups, presence of substituents in the ortho- and meta-position, and lack of a hydroxyl group on the benzene ring reduced the binding affinity. The rtERs resembled the reported binding specificity of the human ER for alkylphenols, although some exceptions were identified.

Almost-dispersionless pulse transport in long quasiuniform spring-mass chains: A different kind of Newton's cradle

NASA Astrophysics Data System (ADS)

Vaia, Ruggero

2018-04-01

Almost-dispersionless pulse transfer between the extremal masses of a uniform harmonic spring-mass chain of arbitrary length can be induced by suitably modifying two masses and their spring's elastic constant at both extrema of the chain. It is shown that a deviation (or a pulse) imposed to the first mass gives rise to a wave packet that, after a time of the order of the chain length, almost perfectly reproduces the same deviation (pulse) at the opposite end, with an amplitude loss that is as small as 1.3% in the infinite-length limit; such a dynamics can continue back and forth again for several times before dispersion cleared the effect. The underlying coherence mechanism is that the initial condition excites a bunch of normal modes with almost equal frequency spacing. This constitutes a possible mechanism for efficient energy transfer, e.g., in nanofabricated structures.

Infinite coherence time of edge spins in finite-length chains

NASA Astrophysics Data System (ADS)

Maceira, Ivo A.; Mila, Frédéric

2018-02-01

Motivated by the recent observation that exponentially long coherence times can be achieved for edge spins in models with strong zero modes, we study the impact of level crossings in finite-length spin chains on the dynamics of the edge spins. Focusing on the X Y spin-1 /2 chain with a transverse or longitudinal magnetic field, two models relevant to understanding recent experimental results on cobalt adatoms, we show that the edge spins can remain coherent for an infinite time even for a finite-length chain if the magnetic field is tuned to a value at which there is a level crossing. Furthermore, we show that the edge spins remain coherent for any initial state for the integrable case of a transverse field because all states have level crossings at the same value of the field, while the coherence time is increasingly large for lower temperatures in the case of a longitudinal field, which is nonintegrable.

Scent gland constituents of the Middle American burrowing python, Loxocemus bicolor (Serpentes: Loxocemidae).

PubMed

Schulze, Thies; Weldon, Paul J; Schulz, Stefan

2017-07-14

Analysis by gas chromatography/mass spectrometry of the scent gland secretions of male and female Middle American burrowing pythons (Loxocemus bicolor) revealed the presence of over 300 components including cholesterol, fatty acids, glyceryl monoalkyl ethers, and alcohols. The fatty acids, over 100 of which were identified, constitute most of the compounds in the secretions and show the greatest structural diversity. They include saturated and unsaturated, unbranched and mono-, di-, and trimethyl-branched compounds ranging in carbon-chain length from 13 to 24. The glyceryl monoethers possess saturated or unsaturated, straight or methyl-branched alkyl chains ranging in carbon-chain length from 13 to 24. Alcohols, which have not previously been reported from the scent glands, possess straight, chiefly saturated carbon chains ranging in length from 13 to 24. Sex or individual differences in secretion composition were not observed. Compounds in the scent gland secretions of L. bicolor may deter offending arthropods, such as ants.

Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments

PubMed Central

Kozłowska, Małgorzata; Tarczewska, Aneta; Jakób, Michał; Bystranowska, Dominika; Taube, Michał; Kozak, Maciej; Czarnocki-Cieciura, Mariusz; Dziembowski, Andrzej; Orłowski, Marek; Tkocz, Katarzyna; Ożyhar, Andrzej

2017-01-01

Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes. Multi-angle light scattering (MALS) and sedimentation equilibrium ultracentrifugation (SE AUC) analyses of the molecular mass of the full-length protein indicated that FKBP39 forms homotetrameric complexes. Molecular models reconstructed from small-angle X-ray scattering (SAXS) revealed that the NPL domain forms a stable, tetrameric core and that FK506-binding domains are linked to it by intrinsically disordered, flexible chains that form tentacle-like segments. Analyses of full-length FKBP39 and its isolated NPL domain suggested that the distal regions of the polypeptide chain influence and determine the quaternary conformation of the nucleoplasmin-like protein. These results provide new insights regarding the conserved structure of nucleoplasmin core domains and provide a potential explanation for the importance of the tetrameric structural organization of full-length nucleoplasmins. PMID:28074868

From single Debye-Hückel chains to polyelectrolyte solutions: Simulation results

NASA Astrophysics Data System (ADS)

Kremer, Kurt

1996-03-01

This lecture will present results from simulations of single weakly charged flexible chains, where the electrostatic part of the interaction is modeled by a Debye-Hückel potential,( with U. Micka, IFF, Forschungszentrum Jülich, 52425 Jülich, Germany) as well as simulations of polyelectrolyte solutions, where the counterions are explicitly taken into account( with M. J. Stevens, Sandia Nat. Lab., Albuquerque, NM 87185-1111) ( M. J. Stevens, K. Kremer, JCP 103), 1669 (1995). The first set of the simulations is meant to clear a recent contoversy on the dependency of the persistence length LP on the screening length Γ. While the analytic theories give Lp ~ Γ^x with either x=1 or x=2, the simulations find for all experimentally accessible chain lengths a varying exponent, which is significantly smaller than 1. This causes serious doubts on the applicability of this model for weakly charged polyelectrolytes in general. The second part deals with strongly charged flexible polyelectrolytes in salt free solution. These simulations are performed for multichain systems. The full Coulomb interactions of the monomers and counterions are treated explicitly. Experimental measurements of the osmotic pressure and the structure factor are reproduced and extended. The simulations reveal a new picture of the chain structure based on calculations of the structure factor, persistence length, end-to-end distance, etc. Even at very low density, the chains show significant bending. Furthermore, the chains contract significantly before they start to overlap. We also show that counterion condensation dramatically alters the chain structure, even for a good solvent backbone.

Equations of state for the fully flexible WCA chains in the fluid and solid phases based on Wertheims-TPT2

NASA Astrophysics Data System (ADS)

Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

2018-03-01

Based on Wertheim's second order thermodynamic perturbation theory (TPT2), equations of state (EOSs) are presented for the fluid and solid phases of tangent, freely jointed spheres. It is considered that the spheres interact with each other through the Weeks-Chandler-Anderson (WCA) potential. The developed TPT2 EOS is the sum of a monomeric reference term and a perturbation contribution due to bonding. MC NVT simulations are performed to determine the structural properties of the reference system in the reduced temperature range of 0.6 ≤ T* ≤ 4.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. Mathematical functions are fitted to the simulation results of the reference system and employed in the framework of Wertheim's theory to develop TPT2 EOSs for the fluid and solid phases. The extended EOSs are compared to the MC NPT simulation results of the compressibility factor and internal energy of the fully flexible chain systems. Simulations are performed for the WCA chain system for chain lengths of up to 15 at T* = 1.0, 1.5, 2.0, 3.0. Across all the reduced temperatures, the agreement between the results of the TPT2 EOS and MC simulations is remarkable. Overall Average Absolute Relative Percent Deviation at T* = 1.0 for the compressibility factor in the entire chain lengths we covered is 0.51 and 0.77 for the solid and fluid phases, respectively. Similar features are observed in the case of residual internal energy.

Equations of state for the fully flexible WCA chains in the fluid and solid phases based on Wertheims-TPT2.

PubMed

Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

2018-03-14

Based on Wertheim's second order thermodynamic perturbation theory (TPT2), equations of state (EOSs) are presented for the fluid and solid phases of tangent, freely jointed spheres. It is considered that the spheres interact with each other through the Weeks-Chandler-Anderson (WCA) potential. The developed TPT2 EOS is the sum of a monomeric reference term and a perturbation contribution due to bonding. MC NVT simulations are performed to determine the structural properties of the reference system in the reduced temperature range of 0.6 ≤ T* ≤ 4.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. Mathematical functions are fitted to the simulation results of the reference system and employed in the framework of Wertheim's theory to develop TPT2 EOSs for the fluid and solid phases. The extended EOSs are compared to the MC NPT simulation results of the compressibility factor and internal energy of the fully flexible chain systems. Simulations are performed for the WCA chain system for chain lengths of up to 15 at T* = 1.0, 1.5, 2.0, 3.0. Across all the reduced temperatures, the agreement between the results of the TPT2 EOS and MC simulations is remarkable. Overall Average Absolute Relative Percent Deviation at T* = 1.0 for the compressibility factor in the entire chain lengths we covered is 0.51 and 0.77 for the solid and fluid phases, respectively. Similar features are observed in the case of residual internal energy.

Evaporation and Hydrocarbon Chain Conformation of Surface Lipid Films

PubMed Central

Sledge, Samiyyah M.; Khimji, Hussain; Borchman, Douglas; Oliver, Alexandria; Michael, Heidi; Dennis, Emily K.; Gerlach, Dylan; Bhola, Rahul; Stephen, Elsa

2016-01-01

Purpose The inhibition of the rate of evaporation (Revap) by surface lipids is relevant to reservoirs and dry eye. Our aim was to test the idea that lipid surface films inhibit Revap. Methods Revap were determined gravimetrically. Hydrocarbon chain conformation and structure were measured using a Raman microscope. Six 1-hydroxyl hydrocarbons (11–24 carbons in length) and human meibum were studied. Reflex tears were obtained from a 62-year-old male. Results The Raman scattering intensity of the lipid film deviated by about 7 % for hydroxyl lipids and varied by 21 % for meibum films across the entire film at a resolution of 5 µm2. All of the surface lipids were ordered. Revap of the shorter chain hydroxyl lipids were slightly (7%) but significantly lower compared with the longer chain hydroxyl lipids. Revap of both groups was essentially similar to that of buffer. A hydroxyl lipid film did not influence Revap over an estimated average thickness range of 0.69 to >6.9 µm. Revap of human tears and buffer with and without human meibum (34.4 µm thick) was not significantly different. Revap of human tears was not significantly different from buffer. Conclusions Human meibum and hydroxyl lipids, regardless of their fluidity, chain length, or thickness did not inhibit Revap of buffer or tears even though they completely covered the surface. It is unlikely that hydroxyl lipids can be used to inhibit Revap of reservoirs. Our data do not support the widely accepted (yet unconfirmed) idea that the tear film lipid layer inhibits Revap of tears. PMID:27395776

Hypothalamic fatty acid sensing in Senegalese sole (Solea senegalensis): response to long-chain saturated, monounsaturated, and polyunsaturated (n-3) fatty acids.

PubMed

Conde-Sieira, Marta; Bonacic, Kruno; Velasco, Cristina; Valente, Luisa M P; Morais, Sofia; Soengas, José L

2015-12-15

We assessed the presence of fatty acid (FA)-sensing mechanisms in hypothalamus of Senegalese sole (Solea senegalensis) and investigated their sensitivity to FA chain length and/or level of unsaturation. Stearate (SA, saturated FA), oleate (OA, monounsaturated FA of the same chain length), α-linolenate [ALA, a n-3 polyunsaturated fatty acid (PUFA) of the same chain length], and eicosapentanoate (EPA, a n-3 PUFA of a larger chain length) were injected intraperitoneally. Parameters related to FA sensing and neuropeptide expression in the hypothalamus were assessed after 3 h and changes in accumulated food intake after 4, 24, and 48 h. Three FA sensing systems characterized in rainbow trout were also found in Senegalese sole and were activated by OA in a way similar to that previously characterized in rainbow trout and mammals. These hypothalamic FA sensing systems were also activated by ALA, differing from mammals, where n-3 PUFAs do not seem to activate FA sensors. This might suggest additional roles and highlights the importance of n-3 PUFA in fish diets, especially in marine species. The activation of FA sensing seems to be partially dependent on acyl chain length and degree of saturation, as no major changes were observed after treating fish with SA or EPA. The activation of FA sensing systems by OA and ALA, but not SA or EPA, is further reflected in the expression of hypothalamic neuropeptides involved in the control of food intake. Both OA and ALA enhanced anorexigenic capacity compatible with the activation of FA sensing systems. Copyright © 2015 the American Physiological Society.

Comprehensive Study on the Impact of the Cation Alkyl Side Chain Length on the Solubility of Water in Ionic Liquids.

PubMed

Kurnia, Kiki A; Neves, Catarina M S S; Freire, Mara G; Santos, Luís M N B F; Coutinho, João A P

2015-10-01

A comprehensive study on the phase behaviour of two sets of ionic liquids (ILs) and their interactions with water is here presented through combining experimental and theoretical approaches. The impact of the alkyl side chain length and the cation symmetry on the water solubility in the asymmetric [C N- 1 C 1 im][NTf 2 ] and symmetric [C N- 1 C N- 1 im][NTf 2 ] series of ILs ( N up to 22), from 288.15 K to 318.15 K and at atmospheric pressure, was studied. The experimental data reveal that the solubility of water in ILs with an asymmetric cation is higher than in those with the symmetric isomer. Several trend shifts on the water solubility as a function of the alkyl side chain length were identified, namely at [C 6 C 1 im][NTf 2 ] for asymmetric ILs and at [C 4 C 4 im][NTf 2 ] and [C 7 C 7 im][NTf 2 ] for the symmetric ILs. To complement the experimental data and to further investigate the molecular-level mechanisms behind the dissolution process, Density Functional Theory calculations, using the Conductor-like Screening Model for Real Solvents (COSMO-RS) and the Electrostatic potential-derived CHelpG, were performed. The COSMO-RS model is able to qualitatively predict water solubility as function of temperature and alkyl chain lengths of both symmetric and asymmetric cations. Furthermore, the model is also capable to predict the somewhat higher water solubility in the asymmetric cation, as well as the trend shift as function of alkyl chain lengths experimentally observed. Both COSMO-RS and the electrostatic potential-derived CHelpG show that the interactions of water and the IL cation take place on the IL polar region, namely on the aromatic head and adjacent methylene groups what explains the differences in water solubility observed for cations with different chain lengths. Furthermore, the CHelpG calculations for the isolated cations in the gas phase indicates that the trend shift of water solubility as function of alkyl chain lengths and the difference of water solubility in symmetric may also result from the partial positive charge distribution/contribution of the cation.

Ameba-like diffusion in two-dimensional polymer melts: how critical exponents determine the structural relaxation

NASA Astrophysics Data System (ADS)

Kreer, Torsten; Meyer, Hendrik; Baschnagel, Joerg

2008-03-01

By means of numerical investigations we demonstrate that the structural relaxation of linear polymers in two dimensional (space-filling) melts is characterized by ameba-like diffusion, where the chains relax via frictional dissipation at their interfacial contact lines. The perimeter length of the contact line determines a new length scale, which does not exist in three dimensions. We show how this length scale follows from the critical exponents, which hence characterize not only the static but also the dynamic properties of the melt. Our data is in agreement with recent theoretical predictions, concerning the time-dependence of single-monomer mean-square displacements and the scaling of concomitant relaxation times with the degree of polymerization. For the latter we demonstrate a density crossover-scaling as an additional test for ameba-like relaxation. We compare our results to the conceptually different Rouse model, which predicts numerically close exponents. Our data can clearly rule out the classical picture as the relevant relaxation mechanism in two-dimensional polymer melts.

Food preference of red devil (Amphilophus labiatus) in the Sermo Reservoir, Kulon Progo Regency

NASA Astrophysics Data System (ADS)

Ariasari, A.; Helmiati, S.; Setyobudi, E.

2018-03-01

Food preference is one of the important information that can be used to know the food chain in order to manage fisheries resources. This study aims to determine the food habits and preference of red devil (Amphilophus labiatus) in the Sermo Reservoir, Kulon Progo Regency. Samples were collected randomly each month from September 2013 to February 2014. Each sample collected was measured its total length, body weight, and determined sex, then dissected to measure the gut length and to observe gut contents. Results showed that red devil is omnivorous (relative gut length = 3.83) with food composition consisted of fish, crustaceans, detritus, phytoplankton, zooplankton, plants, insects, insect’s larvae, Chironomus sp., and annelids. A change occurred in the food preference of red devil, i.e. the young fish prefers to feed Chironomus sp. larvae (86.02 %) whereas the adult fish prefers fish/fish chunk (81.82 %). Trophic level status of red devil showed as carnivorous and niche overlapping between male and female of the adult.

The Effect of Lengthening Cation Ether Tails on Ionic Liquid Properties

DOE PAGES

Lall-Ramnarine, S.; Rodriguez, C.; Fernandez, R.; ...

2016-08-30

In order to explore the effect of multiple ether functionalities on ionic liquid properties, a series of ten pyrrolidinium ionic liquids and ten imidazolium ionic liquids bearing ether and alkyl side chains of varying lengths (4 to 10 atoms in length) were prepared for this study. Their physical properties, such as viscosity, conductivity and thermal profile were measured and compared. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidinium ILs increases there is hardly any increase inmore » the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. These results provide significant insight on the choice of starting materials for researchers designing ILs for specific applications.« less

Overexpression of O-polysaccharide chain length regulators in Gram-negative bacteria using the Wzx-/Wzy-dependent pathway enhances production of defined modal length O-polysaccharide polymers for use as haptens in glycoconjugate vaccines.

PubMed

Hegerle, N; Bose, J; Ramachandran, G; Galen, J E; Levine, M M; Simon, R; Tennant, S M

2018-03-30

O-polysaccharide (OPS) molecules are protective antigens for several bacterial pathogens, and have broad utility as components of glycoconjugate vaccines. Variability in the OPS chain length is one obstacle towards further development of these vaccines. Introduction of sizing steps during purification of OPS molecules of suboptimal or of mixed lengths introduces additional costs and complexity while decreasing the final yield. The overall goal of this study was to demonstrate the utility of engineering Gram-negative bacteria to produce homogenous O-polysaccharide populations that can be used as the basis of carbohydrate vaccines by overexpressing O-polysaccharide chain length regulators of the Wzx-/Wzy-dependent pathway. The O-polysaccharide chain length regulators wzzB and fepE from Salmonella Typhimurium I77 and wzz2 from Pseudomonas aeruginosa PAO1 were cloned and expressed in the homologous organism or in other Gram-negative bacteria. Overexpression of these Wzz proteins in the homologous organism significantly increased the proportion of long or very long chain O-polysaccharides. The same observation was made when wzzB was overexpressed in Salmonella Paratyphi A and Shigella flexneri, and wzz2 was overexpressed in two other strains of P. aeruginosa. Overexpression of Wzz proteins in Gram-negative bacteria using the Wzx/Wzy-dependant pathway for lipopolysaccharide synthesis provides a genetic method to increase the production of an O-polysaccharide population of a defined size. The methods presented herein represent a cost-effective and improved strategy for isolating preferred OPS vaccine haptens, and could facilitate the further use of O-polysaccharides in glycoconjugate vaccine development. © 2018 The Society for Applied Microbiology.

Self-Assemblies of novel molecules, VECAR

NASA Astrophysics Data System (ADS)

Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

2015-03-01

VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length.

PubMed

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S; Du, Yang; Nielsen, Anne K; Byrne, Bernadette; Kobilka, Brian K; Loland, Claus J; Guan, Lan; Chae, Pil Seok

2016-12-14

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C 12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile-lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automated Rugosity Values From High Frequency Multibeam Sonar Data for Benthic Habitat Classification

NASA Astrophysics Data System (ADS)

Diurba, E. S.; Appelgate, B.

2005-12-01

Rugosity literally means wrinkled, or marked with folds and ridges. When applied to seafloor texture, rugosity is one piece of the puzzle that is necessary in order to understand benthic habitats. On a simple level, rugosity is a proxy for habitat complexity and serves as a basis for predicting population density as well as species inhabitants (Friedlander, 1998). Traditionally, rugosity was calculated by draping a chain of known length over the seafloor and comparing the total chain length with the distance the chain covered. The equation Rugosity=100*(length of chain/ actual length of chain) was then applied to get a percent rugosity. However, the process is time consuming and provides little information about the overall bottom roughness. Our objective was to develop a new acoustic method for measuring rugosity and employ this method in conjunction with other types of data, to rapidly characterize the seafloor of a coral reef environment. We developed an automated algorithm to determine the acoustic rugosity of seafloor surfaces from a 240 kHz multibeam sonar data on a ping-by-ping basis. The multibeam data was collected in 2003 during a survey of an anchorage along the NW side of Saipan. This data, collected by the National Oceanic and Atmospheric Administration's (NOAA) Coral Reef Ecosystem Division (CRED), utilized a RESON SeaBat 8101 multibeam sonar that has a vertical resolution of 1.25cm and a range capability of 300m. Each 150 degree ping consists of 101 beams that are each individually logged with x (distance across the ping), and z (depth) coordinates. The rugosity algorithm bins the beams along each ping and uses the x and z coordinates to calculate rugosity. By binning the data solely in the cross-track direction, all rugosity calculations preserve the spatial resolution without distortions from along-track averaging and gridding. This method allows for extremely detailed data sets and quick information about surveyed areas that would otherwise have taken years for divers to manually collect to the same level of resolution. The final product is an objectively derived, quantitative map that is easily comparable to the bathymetry and sidescan data. We present results of this method, using various bin sizes, to show how they compare with other spatial indications of rugosity, as well as with manual and optical rugosity measurements.

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

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

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Tuning the thermal conductivity of solar cell polymers through side chain engineering.

PubMed

Guo, Zhi; Lee, Doyun; Liu, Yi; Sun, Fangyuan; Sliwinski, Anna; Gao, Haifeng; Burns, Peter C; Huang, Libai; Luo, Tengfei

2014-05-07

Thermal transport is critical to the performance and reliability of polymer-based energy devices, ranging from solar cells to thermoelectrics. This work shows that the thermal conductivity of a low band gap conjugated polymer, poly(4,8-bis-alkyloxybenzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-(alkylthieno[3,4-b]thiophene-2-carboxylate)-2,6-diyl) (PBDTTT), for photovoltaic applications can be actively tuned through side chain engineering. Compared to the original polymer modified with short branched side chains, the engineered polymer using all linear and long side chains shows a 160% increase in thermal conductivity. The thermal conductivity of the polymer exhibits a good correlation with the side chain lengths as well as the crystallinity of the polymer characterized using small-angle X-ray scattering (SAXS) experiments. Molecular dynamics simulations and atomic force microscopy are used to further probe the molecular level local order of different polymers. It is found that the linear side chain modified polymer can facilitate the formation of more ordered structures, as compared to the branched side chain modified ones. The effective medium theory modelling also reveals that the long linear side chain enables a larger heat carrier propagation length and the crystalline phase in the bulk polymer increases the overall thermal conductivity. It is concluded that both the length of the side chains and the induced polymer crystallization are important for thermal transport. These results offer important guidance for actively tuning the thermal conductivity of conjugated polymers through molecular level design.

Functional characterization of Gne (UDP-N-acetylglucosamine-4-epimerase), Wzz (chain length determinant), and Wzy (O-antigen polymerase) of Yersinia enterocolitica serotype O:8.

PubMed

Bengoechea, José Antonio; Pinta, Elise; Salminen, Tiina; Oertelt, Clemens; Holst, Otto; Radziejewska-Lebrecht, Joanna; Piotrowska-Seget, Zofia; Venho, Reija; Skurnik, Mikael

2002-08-01

The lipopolysaccharide (LPS) O-antigen of Yersinia enterocolitica serotype O:8 is formed by branched pentasaccharide repeat units that contain N-acetylgalactosamine (GalNAc), L-fucose (Fuc), D-galactose (Gal), D-mannose (Man), and 6-deoxy-D-gulose (6d-Gul). Its biosynthesis requires at least enzymes for the synthesis of each nucleoside diphosphate-activated sugar precursor; five glycosyltransferases, one for each sugar residue; a flippase (Wzx); and an O-antigen polymerase (Wzy). As this LPS shows a characteristic preferred O-antigen chain length, the presence of a chain length determinant protein (Wzz) is also expected. By targeted mutagenesis, we identify within the O-antigen gene cluster the genes encoding Wzy and Wzz. We also present genetic and biochemical evidence showing that the gene previously called galE encodes a UDP-N-acetylglucosamine-4-epimerase (EC 5.1.3.7) required for the biosynthesis of the first sugar of the O-unit. Accordingly, the gene was renamed gne. Gne also has some UDP-glucose-4-epimerase (EC 5.1.3.2) activity, as it restores the core production of an Escherichia coli K-12 galE mutant. The three-dimensional structure of Gne was modeled based on the crystal structure of E. coli GalE. Detailed structural comparison of the active sites of Gne and GalE revealed that additional space is required to accommodate the N-acetyl group in Gne and that this space is occupied by two Tyr residues in GalE whereas the corresponding residues present in Gne are Leu136 and Cys297. The Gne Leu136Tyr and Cys297Tyr variants completely lost the UDP-N-acetylglucosamine-4-epimerase activity while retaining the ability to complement the LPS phenotype of the E. coli galE mutant. Finally, we report that Yersinia Wzx has relaxed specificity for the translocated oligosaccharide, contrary to Wzy, which is strictly specific for the O-unit to be polymerized.

Surface vibrational structure at alkane liquid/vapor interfaces

NASA Astrophysics Data System (ADS)

Esenturk, Okan; Walker, Robert A.

2006-11-01

Broadband vibrational sum frequency spectroscopy (VSFS) has been used to examine the surface structure of alkane liquid/vapor interfaces. The alkanes range in length from n-nonane (C9H20) to n-heptadecane (C17H36), and all liquids except heptadecane are studied at temperatures well above their bulk (and surface) freezing temperatures. Intensities of vibrational bands in the CH stretching region acquired under different polarization conditions show systematic, chain length dependent changes. Data provide clear evidence of methyl group segregation at the liquid/vapor interface, but two different models of alkane chain structure can predict chain length dependent changes in band intensities. Each model leads to a different interpretation of the extent to which different chain segments contribute to the anisotropic interfacial region. One model postulates that changes in vibrational band intensities arise solely from a reduced surface coverage of methyl groups as alkane chain length increases. The additional methylene groups at the surface must be randomly distributed and make no net contribution to the observed VSF spectra. The second model considers a simple statistical distribution of methyl and methylene groups populating a three dimensional, interfacial lattice. This statistical picture implies that the VSF signal arises from a region extending several functional groups into the bulk liquid, and that the growing fraction of methylene groups in longer chain alkanes bears responsibility for the observed spectral changes. The data and resulting interpretations provide clear benchmarks for emerging theories of molecular structure and organization at liquid surfaces, especially for liquids lacking strong polar ordering.

Architecture of the hydrophobic and hydrophilic layers as found from crystal structure analysis of N-benzyl-N,N-dimethylalkylammonium bromides.

PubMed

Hodorowicz, Maciej; Stadnicka, Katarzyna; Czapkiewicz, Jan

2005-10-01

The molecular and crystal structures of N-benzyl-N,N-dimethylalkylammonium bromides monohydrates with chain length n=8-10 have been determined. The crystals are isostructural with the N-benzyl-N,N-dimethyldodecylammonium bromide monohydrate. The structures consist of alternated hydrophobic and hydrophilic layers perpendicular to [001]. The attraction between N+ of the cation head-groups and Br- anions is achieved through weak C_H...Br interactions. The water molecules incorporated into ionic layers are donors for two O_H...Br hydrogen bonds and serve as the acceptors in two weak interactions of C_H...O type. The methylene chains, with the slightly curved general shape, have the extended all-trans conformation. The mutual packing of the chains in the hydrophobic layers is governed by weak C_H...pi interactions.

An effective model of DNA like helicoidal structure: with length fluctuation nonlinearity

NASA Astrophysics Data System (ADS)

Tseytlin, Y. M.

2011-03-01

One of the natural helicoidal nanostructure, which thermomechanical features are studied carefully with the help of different mechanical models, is a DNA cell / molecule. Our study proves that the experimentally determined nonlinear fluctuations of the molecular length of DNA can be better understood by modeling the molecule as a helicoidal pretwisted nanostrip sensor with nonlinear function. The calculations presented here are in good agreement with the experimental data within 10%. Other used by many researchers mechanical models such as an elastic rod, wormlike chain (WLC), accordion bellows, or an elastic core wrapped with rigid wires do not show the possible variance nonlinearity of thermomechanical DNA molecular length fluctuations. We have found that the nonlinear variance of the length fluctuations is an intrinsic property of the micro-nano-sensors with helicoidal shape. This model allows us to estimate the persistence length and twist-stretch coupling of a DNA molecule as well. It also shows the molecule's overwinding possibility at initial stretching with correct numerical representation.

Beating of grafted chains induced by active Brownian particles

NASA Astrophysics Data System (ADS)

Yang, Qiu-song; Fan, Qing-wei; Shen, Zhuang-lin; Xia, Yi-qi; Tian, Wen-de; Chen, Kang

2018-06-01

We study the interplay between active Brownian particles (ABPs) and a "hairy" surface in two-dimensional geometry. We find that the increase of propelling force leads to and enhances inhomogeneous accumulation of ABPs inside the brush region. Oscillation of chain bundles (beating like cilia) is found in company with the formation and disassembly of a dynamic cluster of ABPs at large propelling forces. Meanwhile chains are stretched and pushed down due to the effective shear force by ABPs. The decrease of the average brush thickness with propelling force reflects the growth of the beating amplitude of chain bundles. Furthermore, the beating phenomenon is investigated in a simple single-chain system. We find that the chain swings regularly with a major oscillatory period, which increases with chain length and decreases with the increase of propelling force. We build a theory to describe the phenomenon and the predictions on the relationship between the period and amplitude for various chain lengths, and propelling forces agree very well with simulation data.

Effects of the internal friction and the solvent quality on the dynamics of a polymer chain closure.

PubMed

Yu, Wancheng; Luo, Kaifu

2015-03-28

Using 3D Langevin dynamics simulations, we investigate the effects of the internal friction and the solvent quality on the dynamics of a polymer chain closure. We show that the chain closure in good solvents is a purely diffusive process. By extrapolation to zero solvent viscosity, we find that the internal friction of a chain plays a non-ignorable role in the dynamics of the chain closure. When the solvent quality changes from good to poor, the mean closure time τc decreases by about 1 order of magnitude for the chain length 20 ≤ N ≤ 100. Furthermore, τc has a minimum as a function of the solvent quality. With increasing the chain length N, the minimum of τc occurs at a better solvent. Finally, the single exponential distributions of the closure time in poor solvents suggest that the negative excluded volume of segments does not alter the nearly Poisson statistical characteristics of the process of the chain closure.

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

PubMed

Seol, Yeonee; Li, Jinyu; Nelson, Philip C; Perkins, Thomas T; Betterton, M D

2007-12-15

The wormlike chain (WLC) model currently provides the best description of double-stranded DNA elasticity for micron-sized molecules. This theory requires two intrinsic material parameters-the contour length L and the persistence length p. We measured and then analyzed the elasticity of double-stranded DNA as a function of L (632 nm-7.03 microm) using the classic solution to the WLC model. When the elasticity data were analyzed using this solution, the resulting fitted value for the persistence length p(wlc) depended on L; even for moderately long DNA molecules (L = 1300 nm), this apparent persistence length was 10% smaller than its limiting value for long DNA. Because p is a material parameter, and cannot depend on length, we sought a new solution to the WLC model, which we call the "finite wormlike chain (FWLC)," to account for effects not considered in the classic solution. Specifically we accounted for the finite chain length, the chain-end boundary conditions, and the bead rotational fluctuations inherent in optical trapping assays where beads are used to apply the force. After incorporating these corrections, we used our FWLC solution to generate force-extension curves, and then fit those curves with the classic WLC solution, as done in the standard experimental analysis. These results qualitatively reproduced the apparent dependence of p(wlc) on L seen in experimental data when analyzed with the classic WLC solution. Directly fitting experimental data to the FWLC solution reduces the apparent dependence of p(fwlc) on L by a factor of 3. Thus, the FWLC solution provides a significantly improved theoretical framework in which to analyze single-molecule experiments over a broad range of experimentally accessible DNA lengths, including both short (a few hundred nanometers in contour length) and very long (microns in contour length) molecules.

Self-Consistent Field Theories for the Role of Large Length-Scale Architecture in Polymers

NASA Astrophysics Data System (ADS)

Wu, David

At large length-scales, the architecture of polymers can be described by a coarse-grained specification of the distribution of branch points and monomer types within a molecule. This includes molecular topology (e.g., cyclic or branched) as well as distances between branch points or chain ends. Design of large length-scale molecular architecture is appealing because it offers a universal strategy, independent of monomer chemistry, to tune properties. Non-linear analogs of linear chains differ in molecular-scale properties, such as mobility, entanglements, and surface segregation in blends that are well-known to impact rheological, dynamical, thermodynamic and surface properties including adhesion and wetting. We have used Self-Consistent Field (SCF) theories to describe a number of phenomena associated with large length-scale polymer architecture. We have predicted the surface composition profiles of non-linear chains in blends with linear chains. These predictions are in good agreement with experimental results, including from neutron scattering, on a range of well-controlled branched (star, pom-pom and end-branched) and cyclic polymer architectures. Moreover, the theory allows explanation of the segregation and conformations of branched polymers in terms of effective surface potentials acting on the end and branch groups. However, for cyclic chains, which have no end or junction points, a qualitatively different topological mechanism based on conformational entropy drives cyclic chains to a surface, consistent with recent neutron reflectivity experiments. We have also used SCF theory to calculate intramolecular and intermolecular correlations for polymer chains in the bulk, dilute solution, and trapped at a liquid-liquid interface. Predictions of chain swelling in dilute star polymer solutions compare favorably with existing PRISM theory and swelling at an interface helps explain recent measurements of chain mobility at an oil-water interface. In collaboration with: Renfeng Hu, Colorado School of Mines, and Mark Foster, University of Akron. This work was supported by NSF Grants No. CBET- 0730692 and No. CBET-0731319.

Equivalence of chain conformations in the surface region of a polymer melt and a single Gaussian chain under critical conditions.

PubMed

Skvortsov, A M; Leermakers, F A M; Fleer, G J

2013-08-07

In the melt polymer conformations are nearly ideal according to Flory's ideality hypothesis. Silberberg generalized this statement for chains in the interfacial region. We check the Silberberg argument by analyzing the conformations of a probe chain end-grafted at a solid surface in a sea of floating free chains of concentration φ by the self-consistent field (SCF) method. Apart from the grafting, probe chain and floating chains are identical. Most of the results were obtained for a standard SCF model with freely jointed chains on a six-choice lattice, where immediate step reversals are allowed. A few data were generated for a five-choice lattice, where such step reversals are forbidden. These coarse-grained models describe the equilibrium properties of flexible atactic polymer chains at the scale of the segment length. The concentration was varied over the whole range from φ = 0 (single grafted chain) to φ = 1 (probe chain in the melt). The number of contacts with the surface, average height of the free end and its dispersion, average loop and train length, tail size distribution, end-point and overall segment distributions were calculated for a grafted probe chain as a function of φ, for several chain lengths and substrate∕polymer interactions, which were varied from strong repulsion to strong adsorption. The computations show that the conformations of the probe chain in the melt do not depend on substrate∕polymer interactions and are very similar to the conformations of a single end-grafted chain under critical conditions, and can thus be described analytically. When the substrate∕polymer interaction is fixed at the value corresponding to critical conditions, all equilibrium properties of a probe chain are independent of φ, over the whole range from a dilute solution to the melt. We believe that the conformations of all flexible chains in the surface region of the melt are close to those of an appropriate single chain in critical conditions, provided that one end of the single chain is fixed at the same point as a chain in the melt.

Phase separation of comb polymer nanocomposite melts.

PubMed

Xu, Qinzhi; Feng, Yancong; Chen, Lan

2016-02-07

In this work, the spinodal phase demixing of branched comb polymer nanocomposite (PNC) melts is systematically investigated using the polymer reference interaction site model (PRISM) theory. To verify the reliability of the present method in characterizing the phase behavior of comb PNCs, the intermolecular correlation functions of the system for nonzero particle volume fractions are compared with our molecular dynamics simulation data. After verifying the model and discussing the structure of the comb PNCs in the dilute nanoparticle limit, the interference among the side chain number, side chain length, nanoparticle-monomer size ratio and attractive interactions between the comb polymer and nanoparticles in spinodal demixing curves is analyzed and discussed in detail. The results predict two kinds of distinct phase separation behaviors. One is called classic fluid phase boundary, which is mediated by the entropic depletion attraction and contact aggregation of nanoparticles at relatively low nanoparticle-monomer attraction strength. The second demixing transition occurs at relatively high attraction strength and involves the formation of an equilibrium physical network phase with local bridging of nanoparticles. The phase boundaries are found to be sensitive to the side chain number, side chain length, nanoparticle-monomer size ratio and attractive interactions. As the side chain length is fixed, the side chain number has a large effect on the phase behavior of comb PNCs; with increasing side chain number, the miscibility window first widens and then shrinks. When the side chain number is lower than a threshold value, the phase boundaries undergo a process from enlarging the miscibility window to narrowing as side chain length increases. Once the side chain number overtakes this threshold value, the phase boundary shifts towards less miscibility. With increasing nanoparticle-monomer size ratio, a crossover of particle size occurs, above which the phase separation is consistent with that of chain PNCs. The miscibility window for this condition gradually narrows while the other parameters of the PNCs system are held constant. These results indicate that the present PRISM theory can give molecular-level details of the underlying mechanisms of the comb PNCs. It is hoped that the results can be used to provide useful guidance for the future design control of novel, thermodynamically stable comb PNCs.

Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression.

PubMed

Ziesack, Marika; Rollins, Nathan; Shah, Aashna; Dusel, Brendon; Webster, Gordon; Silver, Pamela A; Way, Jeffrey C

2018-05-15

Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 ( Cp FatB1) (C 8 specificity, lower activity) and Cp FatB2 (C 14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C 8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify Cp FatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a "positive patch" within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from Cp FatB1 into Cp FatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control. IMPORTANCE Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing. Copyright © 2018 American Society for Microbiology.

Nonsimultaneous chains and dominos in kidney- paired donation-revisited.

PubMed

Ashlagi, I; Gilchrist, D S; Roth, A E; Rees, M A

2011-05-01

Since 2008, kidney exchange in America has grown in part from the incorporation of nondirected donors in transplant chains rather than simple exchanges. It is controversial whether these chains should be performed simultaneously 'domino-paired donation', (DPD) or nonsimultaneously 'nonsimultaneous extended altruistic donor, chains (NEAD). NEAD chains create 'bridge donors' whose incompatible recipients receive kidneys before the bridge donor donates, and so risk reneging by bridge donors, but offer the opportunity to create more transplants by overcoming logistical barriers inherent in simultaneous chains. Gentry et al. simulated whether DPD or NEAD chains would produce more transplants when chain segment length was limited to three transplants, and reported that DPD performed at least as well as NEAD chains. As this finding contrasts with the experience of several groups involved in kidney-paired donation, we performed simulations that allowed for longer chain segments and used actual patient data from the Alliance for Paired Donation. When chain segments of 4-6 transplants are allowed in the simulations, NEAD chains produce more transplants than DPD. Our simulations showed not only more transplants as chain length increased, but also that NEAD chains produced more transplants for highly sensitized and blood type O recipients. ©2011 The Authors Journal compilation©2011 The American Society of Transplantation and the American Society of Transplant Surgeons.

Micelle formation of nonionic surfactants in a room temperature ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate: surfactant chain length dependence of the critical micelle concentration.

PubMed

Inoue, Tohru; Yamakawa, Haruka

2011-04-15

Micellization behavior was investigated for polyoxyethylene-type nonionic surfactants with varying chain length (C(n)E(m)) in a room temperature ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF(4)). Critical micelle concentration (cmc) was determined from the variation of (1)H NMR chemical shift with the surfactant concentration. The logarithmic value of cmc decreased linearly with the number of carbon atoms in the surfactant hydrocarbon chain, similarly to the case observed in aqueous surfactant solutions. However, the slope of the straight line is much smaller in bmimBF(4) than in aqueous solution. Thermodynamic parameters for micelle formation estimated from the temperature dependence of cmc showed that the micellization in bmimBF(4) is an entropy-driven process around room temperature. This behavior is also similar to the case in aqueous solution. However, the magnitude of the entropic contribution to the overall micellization free energy in bmimBF(4) is much smaller compared with that in aqueous solution. These results suggest that the micellization in bmimBF(4) proceeds through a mechanism similar to the hydrophobic interaction in aqueous surfactant solutions, although the solvophobic effect in bmimBF(4) is much weaker than the hydrophobic effect. Copyright © 2011 Elsevier Inc. All rights reserved.

Synthesis and Antioxidant Activity of Hydroxytyrosol Alkyl-Carbonate Derivatives.

PubMed

Fernandez-Pastor, Ignacio; Fernandez-Hernandez, Antonia; Rivas, Francisco; Martinez, Antonio; Garcia-Granados, Andres; Parra, Andres

2016-07-22

Three procedures have been investigated for the isolation of tyrosol (1) and hydroxytyrosol (2) from a phenolic extract obtained from the solid residue of olive milling. These three methods, which facilitated the recovery of these phenols, were chemical or enzymatic acetylation, benzylation, and carbomethoxylation, and subsequent carbonylation or acetonation reactions. Several new lipophilic alkyl-carbonate derivatives of hydroxytyrosol have been synthesized, coupling the primary hydroxy group of this phenol, through a carbonate linker, using alcohols with different chain lengths. The antioxidant properties of these lipophilic derivatives have been evaluated by different methods and compared with free hydroxytyrosol (2) and also with the well-known antioxidants BHT and α-tocopherol. Three methods were used for the determination of this antioxidant activity: FRAP and ABTS assays, to test the antioxidant power in hydrophilic media, and the Rancimat test, to evaluate the antioxidant capacity in a lipophilic matrix. These new alkyl-carbonate derivatives of hydroxytyrosol enhanced the antioxidant activity of this natural phenol, with their antioxidant properties also being higher than those of the commercial antioxidants BHT and α-tocopherol. There was no clear influence of the side-chain length on the antioxidant properties of the alkyl-carbonate derivatives of 2, although the best results were achieved mainly by the compounds with a longer chain on the primary hydroxy group of this natural phenolic substance.

Bayesian analysis of experimental epidemics of foot-and-mouth disease.

PubMed Central

Streftaris, George; Gibson, Gavin J.

2004-01-01

We investigate the transmission dynamics of a certain type of foot-and-mouth disease (FMD) virus under experimental conditions. Previous analyses of experimental data from FMD outbreaks in non-homogeneously mixing populations of sheep have suggested a decline in viraemic level through serial passage of the virus, but these do not take into account possible variation in the length of the chain of viral transmission for each animal, which is implicit in the non-observed transmission process. We consider a susceptible-exposed-infectious-removed non-Markovian compartmental model for partially observed epidemic processes, and we employ powerful methodology (Markov chain Monte Carlo) for statistical inference, to address epidemiological issues under a Bayesian framework that accounts for all available information and associated uncertainty in a coherent approach. The analysis allows us to investigate the posterior distribution of the hidden transmission history of the epidemic, and thus to determine the effect of the length of the infection chain on the recorded viraemic levels, based on the posterior distribution of a p-value. Parameter estimates of the epidemiological characteristics of the disease are also obtained. The results reveal a possible decline in viraemia in one of the two experimental outbreaks. Our model also suggests that individual infectivity is related to the level of viraemia. PMID:15306359

[Contamination characteristics of short-chain chlorinated paraffins in edible fish of Shanghai].

PubMed

Jiang, Guo; Chen, Lai-guo; He, Qiu-sheng; Meng, Xiang-zhou; Feng, Yong-bin; Huang, Yu-mei; Tang, Cai-ming

2013-09-01

According to the local habit of eating fish, in a total of 68 samples, 8 kinds of different trophic levels of edible fish collected in Shanghai were determined in terms of concentration and distribution profile of short chain chlorinated paraffin (SCCPs) in muscles to investigate the pollution status of SCCPs in edible fish from the Yangtze River Delta region. The results indicated that the concentrations (dw) of SCCPs in edible fish were in the range of 36-801 ng x g(-1). With the increase in carbon chain length, the concentration of SCCPs decreased. In addition, lower chlorinated (Cl6-Cl8) and shorter chain (Cl10, C11) congeners were the dominant chlorine and carbon homologues groups, respectively, contributing a total relative abundance of 61.46%-82.50% to the total abundance of SCCPs. The levels of SCCPs in fish of Shanghai were in the medium level worldwide, and the distribution pattern was in line with those of the domestic and foreign studies.

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

Graph state generation with noisy mirror-inverting spin chains

NASA Astrophysics Data System (ADS)

Clark, Stephen R.; Klein, Alexander; Bruderer, Martin; Jaksch, Dieter

2007-06-01

We investigate the influence of noise on a graph state generation scheme which exploits a mirror inverting spin chain. Within this scheme the spin chain is used repeatedly as an entanglement bus (EB) to create multi-partite entanglement. The noise model we consider comprises of each spin of this EB being exposed to independent local noise which degrades the capabilities of the EB. Here we concentrate on quantifying its performance as a single-qubit channel and as a mediator of a two-qubit entangling gate, since these are basic operations necessary for graph state generation using the EB. In particular, for the single-qubit case we numerically calculate the average channel fidelity and whether the channel becomes entanglement breaking, i.e. expunges any entanglement the transferred qubit may have with other external qubits. We find that neither local decay nor dephasing noise cause entanglement breaking. This is in contrast to local thermal and depolarizing noise where we determine a critical length and critical noise coupling, respectively, at which entanglement breaking occurs. The critical noise coupling for local depolarizing noise is found to exhibit a power-law dependence on the chain length. For two-qubits we similarly compute the average gate fidelity and whether the ability for this gate to create entanglement is maintained. The concatenation of these noisy gates for the construction of a five-qubit linear cluster state and a Greenberger Horne Zeilinger state indicates that the level of noise that can be tolerated for graph state generation is tightly constrained.

Size, shape, and diffusivity of a single Debye-Hückel polyelectrolyte chain in solution.

PubMed

Soysa, W Chamath; Dünweg, B; Prakash, J Ravi

2015-08-14

Brownian dynamics simulations of a coarse-grained bead-spring chain model, with Debye-Hückel electrostatic interactions between the beads, are used to determine the root-mean-square end-to-end vector, the radius of gyration, and various shape functions (defined in terms of eigenvalues of the radius of gyration tensor) of a weakly charged polyelectrolyte chain in solution, in the limit of low polymer concentration. The long-time diffusivity is calculated from the mean square displacement of the centre of mass of the chain, with hydrodynamic interactions taken into account through the incorporation of the Rotne-Prager-Yamakawa tensor. Simulation results are interpreted in the light of the Odjik, Skolnick, Fixman, Khokhlov, and Khachaturian blob scaling theory (Everaers et al., Eur. Phys. J. E 8, 3 (2002)) which predicts that all solution properties are determined by just two scaling variables-the number of electrostatic blobs X and the reduced Debye screening length, Y. We identify three broad regimes, the ideal chain regime at small values of Y, the blob-pole regime at large values of Y, and the crossover regime at intermediate values of Y, within which the mean size, shape, and diffusivity exhibit characteristic behaviours. In particular, when simulation results are recast in terms of blob scaling variables, universal behaviour independent of the choice of bead-spring chain parameters, and the number of blobs X, is observed in the ideal chain regime and in much of the crossover regime, while the existence of logarithmic corrections to scaling in the blob-pole regime leads to non-universal behaviour.

Acyl chain conformational ordering of individual components in liquid-crystalline bilayers of mixtures of phosphatidylcholines and phosphatidic acids. A comparative FTIR and 2H NMR study

NASA Astrophysics Data System (ADS)

Ziegler, Wolfgang; Blume, Alfred

1995-09-01

The conformational ordering of the acyl chains of all possible binary 1:1 mixtures containing the phospholipids DMPC, DMPA, DPPC, and DPPA was investigated using FTIR and 2H NMR spectroscopy. One of the components was always labelled with perdeuterated chains to be able to observe the individual behaviour of the two components. From the temperature dependence of the frequencies of the symmetric and antisymmetric CH 2- and CD 2-stretching vibrations the transition temperatures were determined. The integral intensities of the conformation sensitive CH 2-wagging bands at ca. 1368 cm -1(gtg' and gtg sequences), 1356 cm -1 (double gauche), and 1342 cm -1 (end gauche) can be converted to numbers of gauche conformers per acyl chain using calibration factors published by Senak et al. J. Phys. Chem. 95 (1991) 2565. The 2H NMR quadrupolar splittings of the CD 2-segments of the perdeuterated lipid components are affected not only by trans-gauche isomerizations but also by long axis rotations and restricted wobbling motions of the acyl chains. The values of the average gauche probability overlinep3 from FTIR spectroscopy and the average order parameters overlineSCD, the order parameter of the terminal methyl groups SCDCD 3 and the average order parameter for the plateau region overlineSCDPlat of components in the mixtures are compared to those of the pure lipids evaluated in a previous publication Tuchtenhagen et al. Eur. Biophys. J. 23 (1994) 323. The conformational behaviour of lipids in mixtures is mainly influenced by head groups interactions, PAs always being more ordered than the corresponding PCs. Depending on absolute chain length and on chain length differences between the two components different conformational behaviour is observed for the two components in the mixtures, indicating non-ideal mixing and formation of micro-domains in the liquid-crystalline phase. Increases in order at the chain ends with a concomitant decrease in probabilities for end gauche conformations give hints to chain interdigitation in the liquid-crystalline phase.

Electron transfer of quinone self-assembled monolayers on a gold electrode.

PubMed

Nagata, Morio; Kondo, Masaharu; Suemori, Yoshiharu; Ochiai, Tsuyoshi; Dewa, Takehisa; Ohtsuka, Toshiaki; Nango, Mamoru

2008-06-15

Dialkyl disulfide-linked naphthoquinone, (NQ-Cn-S)2, and anthraquinone, (AQ-Cn-S)2, derivatives with different spacer alkyl chains (Cn: n=2, 6, 12) were synthesized and these quinone derivatives were self-assembled on a gold electrode. The formation of self-assembled monolayers (SAMs) of these derivatives on a gold electrode was confirmed by infrared reflection-absorption spectroscopy (IR-RAS). Electron transfer between the derivatives and the gold electrode was studied by cyclic voltammetry. On the cyclic voltammogram a reversible redox reaction between quinone (Q) and hydroquinone (QH2) was clearly observed under an aqueous condition. The formal potentials for NQ and AQ derivatives were -0.48 and -0.58 V, respectively, that did not depend on the spacer length. The oxidation and reduction peak currents were strongly dependent on the spacer alkyl chain length. The redox behavior of quinone derivatives depended on the pH condition of the buffer solution. The pH dependence was in agreement with a theoretical value of E 1/2 (mV)=E'-59pH for 2H+/2e(-) process in the pH range 3-11. In the range higher than pH 11, the value was estimated with E 1/2 (mV)=E'-30pH , which may correspond to H+/2e(-) process. The tunneling barrier coefficients (beta) for NQ and AQ SAMs were determined to be 0.12 and 0.73 per methylene group (CH2), respectively. Comparison of the structures and the alkyl chain length of quinones derivatives on these electron transfers on the electrode is made.

Influence of chain length and double bond on the aqueous behavior of choline carboxylate soaps.

PubMed

Rengstl, Doris; Diat, Olivier; Klein, Regina; Kunz, Werner

2013-02-26

In preceding studies, we demonstrated that choline carboxylates ChC(m) with alkyl chain lengths of m = 12 - 18 are highly water-soluble (for m = 12, soluble up to 93 wt % soap and 0 °C). In addition, choline soaps are featured by an extraordinary lyotropic phase behavior. With decreasing water concentration, the following phases were found: micellar phase (L(1)), discontinuous cubic phase (I(1)' and I(1)"), hexagonal phase (H(1)), bicontinuous cubic phase (V(1)), and lamellar phase (L(α)). The present work is also focused on the lyotropic phase behavior of choline soaps but with shorter alkyl chains or different alkyl chain properties. We have investigated the aqueous phase behavior of choline soaps with C(8) and C(10) chain-lengths (choline octanoate and choline decanoate) and with a C(18) chain-length with a cis-double bond (choline oleate). We found that choline decanoate follows the lyotropic phase behavior of the longer-chain homologues mentioned above. Choline octanoate in water shows no discontinuous cubic phases, but an extended, isotropic micellar solution phase. In addition, choline octanoate is at the limit between a surfactant and a hydrotrope. The double bond in choline oleate leads also to a better solubility in water and a decrease of the solubilization temperature. It also influences the Gaussian curvature of the aggregates which results in a loss of discontinuous cubic phases in the binary phase diagram. The different lyotropic mesophases were identified by the penetration scan technique with polarizing light microscope and visual observations. To clarify the structural behavior small (SAXS) and wide (WAXS) angle X-ray scattering were performed. To further characterize the extended, isotropic micellar solution phase in the binary phase diagram of choline octanoate viscosity and conductivity measurements were also carried out.

Studies on the solvation dynamics of coumarin 153 in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: dependence on alkyl chain length.

PubMed

Das, Sudhir Kumar; Sarkar, Moloy

2012-08-06

Steady-state and time-resolved fluorescence behavior of coumarin 153 (C153) is investigated in a series of 1-ethyl-3-methylimidazolium alkylsulfate ([C(2)mim][C(n)OSO(3)]) ionic liquids differing only in the length of the linear alkyl chain (n = 4, 6, and 8) in the anion. The aim of the present study is to understand the role of alkyl chain length in solute rotation and solvation dynamics of C153 in these ionic liquids. The blueshift observed in the steady-state absorption and emission maxima of C153 on going from the C(4)OSO(3) to the C(8)OSO(3) system indicates increasing nonpolar character of the microenvironment of the solute with increasing length of the alkyl side chain of the anion of the ionic liquids. The average solvation time is also found to increase on changing the substituent from butyl to octyl, and this is attributed to the increase in the bulk viscosity of the ILs. A steady blueshift of the time-zero maximum of the fluorescence spectrum with increasing alkyl chain length also indicates that the probe molecule experiences a less polar environment in the early part of the dynamics. Rotational dynamics of C153 are also analyzed by using the Stokes-Einstein-Debye (SED), Gierer-Wirtz (GW), and Dote-Kivelson-Schwartz (DKS) theories. Analyses of the results seem to suggest decoupling of the rotational motion of the probe from solvent viscosity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

DOE PAGES

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora; ...

2015-11-03

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality is studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro-optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro-optical properties which are critical in their current and potential uses. The current study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonylmore » PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent whereas in water and implicit poor solvent, the nonyl side chains are collapsed towards the PPE backbone. Thus, rotation around the aromatic ring is fast and no long range correlations are seen within the backbone.« less

Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

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

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality is studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro-optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro-optical properties which are critical in their current and potential uses. The current study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonylmore » PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent whereas in water and implicit poor solvent, the nonyl side chains are collapsed towards the PPE backbone. Thus, rotation around the aromatic ring is fast and no long range correlations are seen within the backbone.« less

Tandem catalysis for the preparation of cylindrical polypeptide brushes.

PubMed

Rhodes, Allison J; Deming, Timothy J

2012-11-28

Here, we report a method for synthesis of cylindrical copolypeptide brushes via N-carboxyanhydride (NCA) polymerization utilizing a new tandem catalysis approach that allows preparation of brushes with controlled segment lengths in a straightforward, one-pot procedure requiring no intermediate isolation or purification steps. To obtain high-density brush copolypeptides, we used a "grafting from" approach where alloc-α-aminoamide groups were installed onto the side chains of NCAs to serve as masked initiators. These groups were inert during cobalt-initiated NCA polymerization and gave allyloxycarbonyl-α-aminoamide-substituted polypeptide main chains. The alloc-α-aminoamide groups were then activated in situ using nickel to generate initiators for growth of side-chain brush segments. This use of stepwise tandem cobalt and nickel catalysis was found to be an efficient method for preparation of high-chain-density, cylindrical copolypeptide brushes, where both the main chains and side chains can be prepared with controlled segment lengths.

Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

DOE PAGES

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

2016-04-06

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Inulin-enriched dairy desserts: physicochemical and sensory aspects.

PubMed

González-Tomás, L; Bayarri, S; Costell, E

2009-09-01

The aim of this work was to study how adding inulin of different average chain lengths (long-chain, native, and short-chain inulin) at a concentration of 7.5% (wt/wt) would affect the physicochemical and sensory characteristics of starch-based dairy desserts formulated with either skim or whole milk. The results have shown that the effect of adding 7.5% inulin of different average chain length can give rise to products with different rheological behavior and different sensory characteristics. The skim milk sample with long-chain inulin and the whole milk sample without inulin showed similar flow behavior. Both samples were perceived to have the same creaminess and consistency intensity, but addition of long-chain inulin increased roughness intensity and, consequently, the sensory quality could be negatively affected. The information obtained may be of great interest in designing new products with nutritional and sensory characteristics that meet consumer demands.

Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate

PubMed Central

Cardinali-Rezende, Juliana; Alexandrino, Paulo Moises Raduan; Nahat, Rafael Augusto Theodoro Pereira de Souza; Sant’Ana, Débora Parrine Vieira; Silva, Luiziana Ferreira; Gomez, José Gregório Cabrera

2015-01-01

Pseudomonas sp. LFM046 is a medium-chain-length polyhydroxyalkanoate (PHAMCL) producer capable of using various carbon sources (carbohydrates, organic acids, and vegetable oils) and was first isolated from sugarcane cultivation soil in Brazil. The genome sequence was found to be 5.97 Mb long with a G+C content of 66%. PMID:26294616

DATA COLLECTION CONSTRAINTS FOR THE USE OF LENGTH HETEROGENEITY POLYMERASE CHAIN REACTION (LH-PCR) AS AN INDICATOR OF STREAM SANITARY AND ECOLOGICAL CONDITION

EPA Science Inventory

This study is part of a larger project for the development of bacterial indicators of stream sanitary and ecological condition. Here we report preliminary research on the use of Length Heterogeneity Polymerase Chain Reaction (LH-PCR), which discriminates among 16S rRNA genes bas...

Confined wormlike chains in external fields

NASA Astrophysics Data System (ADS)

Morrison, Greg

The confinement of biomolecules is ubiquitous in nature, such as the spatial constraints of viral encapsulation, histone binding, and chromosomal packing. Advances in microfluidics and nanopore fabrication have permitted powerful new tools in single molecule manipulation and gene sequencing through molecular confinement as well. In order to fully understand and exploit these systems, the ability to predict the structure of spatially confined molecules is essential. In this talk, I describe a mean field approach to determine the properties of stiff polymers confined to cylinders and slits, which is relevant for a variety of biological and experimental conditions. I show that this approach is able to not only reproduce known scaling laws for confined wormlike chains, but also provides an improvement over existing weakly bending rod approximations in determining the detailed chain properties (such as correlation functions). Using this approach, we also show that it is possible to study the effect of an externally applied tension or static electric field in a natural and analytically tractable way. These external perturbations can alter the scaling laws and introduce important new length scales into the system, relevant for histone unbinding and single-molecule analysis of DNA.

Crazing of nanocomposites with polymer-tethered nanoparticles

DOE PAGES

Meng, Dong; Kumar, Sanat K.; Ge, Ting; ...

2016-09-07

The crazing behavior of polymer nanocomposites formed by blending polymer grafted nanoparticles with an entangled polymer melt is studied by molecular dynamics simulations. We focus on the three key differences in the crazing behavior of a composite relative to the pure homopolymer matrix, namely, a lower yield stress, a smaller extension ratio, and a grafted chain length dependent failure stress. The yield behavior is found to be mostly controlled by the local nanoparticle-grafted polymer interfacial energy, with the grafted polymer-polymer matrix interfacial structure being of little to no relevance. Increasing the attraction between nanoparticle core and the grafted polymer inhibitsmore » void nucleation and leads to a higher yield stress. In the craze growth regime, the presence of “grafted chain” sections of ≈100 monomers alters the mechanical response of composite samples, giving rise to smaller extension ratios and higher drawing stresses than for the homopolymer matrix. As a result, the dominant failure mechanism of composite samples depends strongly on the length of the grafted chains, with disentanglement being the dominant mechanism for short chains, while bond breaking is the failure mode for chain lengths >10N e, where N e is the entanglement length.« less

Stability of polyelectrolyte-coated iron nanoparticles for T2-weighted magnetic resonance imaging

NASA Astrophysics Data System (ADS)

McGrath, Andrew J.; Dolan, Ciaran; Cheong, Soshan; Herman, David A. J.; Naysmith, Briar; Zong, Fangrong; Galvosas, Petrik; Farrand, Kathryn J.; Hermans, Ian F.; Brimble, Margaret; Williams, David E.; Jin, Jianyong; Tilley, Richard D.

2017-10-01

Iron nanoparticles are highly-effective magnetic nanoparticles for T2 magnetic resonance imaging (MRI). However, the stability of their magnetic properties is dependent on good protection of the iron core from oxidation in aqueous media. Here we report the synthesis of custom-synthesized phosphonate-grafted polyelectrolytes (PolyM3) of various chain lengths, for efficient coating of iron nanoparticles with a native iron oxide shell. The size of the nanoparticle-polyelectrolyte assemblies was investigated by transmission electron microscopy and dynamic light scattering, while surface attachment was confirmed by Fourier transform infrared spectroscopy. Low cytotoxicity was observed for each of the nanoparticle-polyelectrolyte ("Fe-PolyM3") assemblies, with good cell viability (>80%) remaining up to 100 μg mL-1 Fe in HeLa cells. When applied in T2-weighted MRI, corresponding T2 relaxivities (r2) of the Fe-PolyM3 assemblies were found to be dependent on the chain length of the polyelectrolyte. A significant increase in contrast was observed when polyelectrolyte chain length was increased from 6 to 65 repeating units, implying a critical chain length required for stabilization of the α-Fe nanoparticle core.

Electrostatic stiffening and induced persistence length for coassembled molecular bottlebrushes

NASA Astrophysics Data System (ADS)

Storm, Ingeborg M.; Stuart, Martien A. Cohen; de Vries, Renko; Leermakers, Frans A. M.

2018-03-01

A self-consistent field analysis for tunable contributions to the persistence length of isolated semiflexible polymer chains including electrostatically driven coassembled deoxyribonucleic acid (DNA) bottlebrushes is presented. When a chain is charged, i.e., for polyelectrolytes, there is, in addition to an intrinsic rigidity, an electrostatic stiffening effect, because the electric double layer resists bending. For molecular bottlebrushes, there is an induced contribution due to the grafts. We explore cases beyond the classical phantom main-chain approximation and elaborate molecularly more realistic models where the backbone has a finite volume, which is necessary for treating coassembled bottlebrushes. We find that the way in which the linear charge density or the grafting density is regulated is important. Typically, the stiffening effect is reduced when there is freedom for these quantities to adapt to the curvature stresses. Electrostatically driven coassembled bottlebrushes, however, are relatively stiff because the chains have a low tendency to escape from the compressed regions and the electrostatic binding force is largest in the convex part. For coassembled bottlebrushes, the induced persistence length is a nonmonotonic function of the polymer concentration: For low polymer concentrations, the stiffening grows quadratically with coverage; for semidilute polymer concentrations, the brush chains retract and regain their Gaussian size. When doing so, they lose their induced persistence length contribution. Our results correlate well with observed physical characteristics of electrostatically driven coassembled DNA-bioengineered protein-polymer bottlebrushes.

L-cysteine-derived ambidextrous gelators of aromatic solvents and ethanol/water mixtures.

PubMed

Pal, Amrita; Dey, Joykrishna

2013-02-19

A series of L-cysteine-derived double hydrocarbon chain amphiphilic gelators L-(3-alkyl-carbamoylsulfanyl)-2-(3-alkylurido)propionic acid with different hydrocarbon chain lengths (C6-C16) was designed and synthesized. These gelators efficiently gelate only aromatic solvents. The gelation ability increased with the increase of chain length up to C14, but then it dropped with further increase of chain length. The C12 and C14 derivatives also gelled ethanol/water mixtures. The gels were characterized by a number of methods, including FT-IR, NMR, and XRD spectroscopy, electron microscopy, and rheology. The amphiphiles were observed to form either flat lamellar or ribbonlike aggregates in aromatic solvents as well as in ethanol/water mixtures. The gelation in all the solvents employed was observed to be thermoreversible. The gel-to-sol transition temperature as well as mechanical strength of the organogels were observed to increase with the hydrocarbon chain length. Both types of gels of C8-C16 amphiphiles have gel-to-sol transition temperatures above the physiological temperature (310 K). FT-IR and variable temperature (1)H NMR measurements suggested that van der Waals interactions have major contribution in the gelation process. The gel-to-sol transition temperature and mechanical strength of the organogels in ethanol/water mixtures was observed to be higher than those of benzene organogel.

Degradation of linear alkylabenzene sulfonate (LAS) and its compounds in Donghu Lake (Hubei, P.R.C.) determined by high performance liquid chromatography (HPLC)

NASA Astrophysics Data System (ADS)

Ayfer, Yediler; Xu, Ying; Zhang, Yongyuan; Chen, Junjian

1990-06-01

Commercial linear alkylbenzene sulfonate (LAS), mixture of alkylchain lengths and phenyl position isomers (C10-C13), is widely used as a major constituent of household and industrial detergents in the People's Republic of China. Degradation process and behaviour of LAS compounds during an 82-hour lake water die-away study, with an added LAS concentration of 1.5mg·L-1, was quantified and accomplished by HPLO-UV after extractionon the SepPek C18 reversed-phase cartridges. The degradation rate became progressively faster with increasing chain length. The technique described in this study is fast, sensitive and specific, and can be used to determine low levels of LAS and for establishing water quality criteria and standards relating to LAS and its compounds.

Geranylgeranyl diphosphate synthases from Scoparia dulcis and Croton sublyratus. cDNA cloning, functional expression, and conversion to a farnesyl diphosphate synthase.

PubMed

Kojima, N; Sitthithaworn, W; Viroonchatapan, E; Suh, D Y; Iwanami, N; Hayashi, T; Sankaw, U

2000-07-01

cDNAs encoding geranylgeranyl diphosphate synthase (GGPPS) of two diterpene producing plants, Scoparia dulcis and Croton sublyratus, were isolated using the homology-based polymerase chain reaction method. Both cloned genes showed high amino acid sequence homology (60-70%) to other plant GGPPSs and contained highly conserved aspartate-rich motifs. The obtained clones were functionally expressed in Escherichia coli and showed sufficient GGPPS activity to catalyze the condensation of farnesyl diphosphate (FPP) and isopentenyl diphosphate to form geranylgeranyl diphosphate. To investigate the factor determining the product chain length of plant GGPPSs, S. dulcis GGPPS mutants in which either the small amino acids at the fourth and fifth positions before the first aspartate-rich motif (FARM) were replaced with aromatic amino acids or in which two additional amino acids in FARM were deleted were constructed. Both mutants behaved like FPPS-like enzymes and almost exclusively produced FPP when dimethylallyl diphosphate was used as a primer substrate, and failed to accept FPP as a primer substrate. These results indicate that both small amino acids at the fourth and fifth positions before FARM and the amino acid insertion in FARM play essential roles in product length determination in plant GGPPSs.

Novel phytoceramides containing fatty acids of diverse chain lengths are better than a single C18-ceramide N-stearoyl phytosphingosine to improve the physiological properties of human stratum corneum.

PubMed

Oh, Myoung Jin; Cho, Young Hoon; Cha, So Yoon; Lee, Eun Ok; Kim, Jin Wook; Kim, Sun Ki; Park, Chang Seo

2017-01-01

Ceramides in the human stratum corneum (SC) are a mixture of diverse N -acylated fatty acids (FAs) with different chain lengths. C24 is the major class of FAs of ceramides. However, there are also other classes of ceramides with diverse chain lengths of FAs, and these lengths generally range from C16 to C26. This study aimed to prepare several types of phytoceramide containing diverse chain lengths of N -acylated FAs and compare them with C18-ceramide N -stearoyl phytosphingosine (NP) in terms of their effects on the physiological properties of the SC. We chose natural oils, such as horse fat oil, shea butter, sunflower oil, and a mixture of macadamia nut, shea butter, moringa, and meadowfoam seed oil, as sources of FAs and phytosphingosine as a sphingoid backbone to synthesize diverse phytoceramides. Each phytoceramide exhibited a distinctive formation of the lamellar structure, and their FA profiles were similar to those of their respective natural oil. The skin barrier properties, as analyzed in human skin, clearly demonstrated that all the phytoceramides improved the recovery rate of the damaged SC and enhanced hydration better than C18-ceramide NP did. In conclusion, natural oil-derived phytoceramides could represent a novel class of ceramides for cosmetic applications in the development of an ideal skin barrier moisturizer.

Entanglement Length in Miscible Blends of cis-Polyisoprene and Poly(ptert-butylstyrene)

NASA Astrophysics Data System (ADS)

Watanabe, Hiroshi; Matsumiya, Yumi

In miscible polymer blends, the entanglement length is common for the components, but its changes with the composition w remain unclear. For this problem, this study analyzed viscoelastic data for miscible blends of cis-polyisoprene (PI) and poly(ptert-butylstyrene) (PtBS), considering the basic feature that the local relaxation is determined only by wPI. On the basis of this feature, a series of unentangled low- M PI/PtBS blends having various M and a given wPI were utilized as references for well-entangled high- M PI/PtBS blends having the same wPI, and the modulus data of the references were subtracted from the high- M blend data. For an optimally chosen reference, the storage modulus Ge'of the high- M blends obtained after the subtraction exhibited a clear entanglement plateau GN and the corresponding Ge' ' decreased in proportion to 1/ ω at high frequencies ω. Thus, the onset of entanglement relaxation was detected. The GN values were well described by a linear mixing rule of the entanglement length with the number fraction of Kuhn segments of the components being utilized as the averaging weight. This result, not explained by a mean-field picture of entanglement, is discussed in relation to local packing of bulky PtBS chains and skinny PI chains.

Particle stabilized aqueous foams at different length scales: synergy between silica particles and alkylamines.

PubMed

Carl, Adrian; Bannuscher, Anne; von Klitzing, Regine

2015-02-10

Nanoparticles can be efficient foaming agents. Yet, the detailed mechanisms of foam stabilization by these particles remain unclear. In most cases, the foamability and foam stability of a system have to be determined empirically. We used a multiscale approach to reveal how the microscopic properties of the nanoparticle dispersion are translated into their foaming behavior at the macroscopic scale. As a model system we used silica nanoparticles that were hydrophobized by the in situ adsorption of short-chain alkylamines of chain length C5 to C8. We used fluorescence spectroscopy and electrophoretic mobility measurements to characterize the bulk behavior of the nanoparticles with adsorbed amines. The interfacial behavior was probed by compressing particle monolayers while monitoring the surface tension. The macroscopic foamability and foam stability were evaluated. There are strong correlations between the system properties at all length scales. The most prominent effects are observed at a critical bulk concentration of amines at which the nanoparticles start to aggregate due to hydrophobic interactions. Our study shows how the foam properties are related to the features of the bulk dispersions and to the ordering of particles at the air/water interface. The present results help to understand the surfactant concentration dependent stages of foaming behavior of in situ hydrophobized nanoparticles.

A best on-line algorithm for single machine scheduling the equal length jobs with the special chain precedence and delivery time

NASA Astrophysics Data System (ADS)

Gu, Cunchang; Mu, Yundong

2013-03-01

In this paper, we consider a single machine on-line scheduling problem with the special chains precedence and delivery time. All jobs arrive over time. The chains chainsi arrive at time ri , it is known that the processing and delivery time of each job on the chain satisfy one special condition CD a forehand: if the job J(i)j is the predecessor of the job J(i)k on the chain chaini, then they satisfy p(i)j = p(i)k = p >= qj >= qk , i = 1,2, ---,n , where pj and qj denote the processing time and the delivery time of the job Jj respectively. Obviously, if the arrival jobs have no chains precedence, it shows that the length of the corresponding chain is 1. The objective is to minimize the time by which all jobs have been delivered. We provide an on-line algorithm with a competitive ratio of √2 , and the result is the best possible.

Polyphenol fatty acid esters as serine protease inhibitors: a quantum-chemical QSAR analysis.

PubMed

Viskupicova, Jana; Danihelova, Martina; Majekova, Magdalena; Liptaj, Tibor; Sturdik, Ernest

2012-12-01

We investigated the ability of polyphenol fatty acid esters to inhibit the activity of serine proteases trypsin, thrombin, elastase and urokinase. Potent protease inhibition in micromolar range was displayed by rutin and rutin derivatives esterified with medium and long chain, mono- and polyunsaturated fatty acids (1e-m), followed by phloridzin and esculin esters with medium and long fatty acid chain length (2a-d, 3a-d), while unmodified compounds showed only little or no effect. QSAR study of the compounds tested provided the most significant parameters for individual inhibition activities, i.e. number of hydrogen bond donors for urokinase, molecular volume for thrombin, and solvation energy for elastase. According to the statistical analysis, the action of elastase inhibitors is opposed to those of urokinase and thrombin. Cluster analysis showed two groups of compounds: original polyphenols together with rutin esters with short fatty acid chain length and rutin esters with long fatty acid chain length.

Characterization of medium-chain-length polyhydroxyalkanoate biosynthesis by Pseudomonas mosselii TO7 using crude glycerol.

PubMed

Liu, Ming-Hsu; Chen, Yi-Jr; Lee, Chia-Yin

2018-03-01

Polyhydroxyalkanoates (PHAs) are biopolyesters produced by microorganisms that are environmentally friendly. PHAs can be used to replace traditional plastic to reduce environmental pollution in various fields. PHA production costs are high because PHA must be produced from a carbon substrate. The purpose of this study was to find the strain that can used the BDF by-product as the sole carbon source to produce high amounts of medium-chain-length PHA. Three isolates were evaluated for potential PHA production by using biodiesel-derived crude glycerol as the sole carbon source. Among them, Pseudomonas mosselii TO7 yielded high PHA content. The PHA produced from P. mosselii TO7 were medium-chain-length-PHAs. The PHA content of 48% cell dry weight in 48 h with a maximum PHA productivity of 13.16 mg PHAs L -1  h -1 . The narrow polydispersity index value of 1.3 reflected the homogeneity of the polymer chain, which was conducive to industrial applications.

4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

PubMed Central

Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

2009-01-01

Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4N, 4S and 4O derivatives vs. μ-oxo dimeric heme, measure binding constants for monomeric vs. dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs. CQR malaria. PMID:18512900

4-N-, 4-S-, and 4-O-chloroquine analogues: influence of side chain length and quinolyl nitrogen pKa on activity vs chloroquine resistant malaria.

PubMed

Natarajan, Jayakumar K; Alumasa, John N; Yearick, Kimberly; Ekoue-Kovi, Kekeli A; Casabianca, Leah B; de Dios, Angel C; Wolf, Christian; Roepe, Paul D

2008-06-26

Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.

Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length.

PubMed

Kobayashi, Shinya; Fujii, Sotaro; Koga, Aya; Wakai, Satoshi; Matubayasi, Nobuyuki; Sambongi, Yoshihiro

2017-07-01

Reversible denaturation of Pseudomonas aeruginosa cytochrome c 551 (PAc 551 ) could be followed using five systematic urea derivatives that differ in the alkyl chain length, i.e. urea, N-methylurea (MU), N-ethylurea (EU), N-propylurea (PU), and N-butylurea (BU). The BU concentration was the lowest required for the PAc 551 denaturation, those of PU, EU, MU, and urea being gradually higher. Furthermore, the accessible surface area difference upon PAc 551 denaturation caused by BU was found to be the highest, those by PU, EU, MU, and urea being gradually lower. These findings indicate that urea derivatives with longer alkyl chains are stronger denaturants. In this study, as many as five systematic urea derivatives could be applied for the reversible denaturation of a single protein, PAc 551 , for the first time, and the effects of the alkyl chain length on protein denaturation were systematically verified by means of thermodynamic parameters.

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

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

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

DOE PAGES

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.; ...

2017-10-25

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Re-assessing the role of plant community change and climate in the PETM n-alkane record

NASA Astrophysics Data System (ADS)

Bush, R. T.; Baczynski, A. A.; McInerney, F. A.; Chen, D.

2012-12-01

The terrestrial leaf wax n-alkane record of the Paleocene-Eocene Thermal Maximum (PETM) in the Bighorn Basin, Wyoming, shows large excursions in both carbon isotope (δ13C) values and n-alkane average chain length (ACL). At the onset of the PETM, ACL values increase from ~28.5 to ~30.1 while the negative carbon isotope excursion (CIE) is 4-6‰ in magnitude and larger than δ13C records from other materials. It has been hypothesized previously that both the ACL excursion and the large magnitude of the CIE were caused by a concurrent turnover in the local flora from a mixed conifer/angiosperm community before the PETM to a different suite of angiosperm species during the PETM. Here, we present the results of a meta-analysis of data (>2000 data from 89 sources, both published and unpublished) on n-alkane amounts and chain length distributions in modern plants from around the world. We applied the data in two sets of comparisons: 1) within and among plant groups such as herbs and graminoids, and 2) between plants and climate, using reported collection locations for outdoor plants and climate values generated via GIS extraction of WorldClim modeled data. We show that angiosperms, as group, produce more n-alkanes than do gymnosperms by 1-2 orders of magnitude, and this means that the gymnosperm contribution to a mixed soil n-alkane pool would be negligible, even in an ecosystem where gymnosperms dominated (i.e. the pre/post-PETM ecosystems). The modern plant data also demonstrate that turnover of the plant community during the PETM, even among only the angiosperm species, is likely not the source of the observed ACL excursion. First, we constructed "representative" groups of PETM and pre/post-PETM communities using living relative species at the Chicago Botanic Garden and find no significant difference in chain length distributions between the two groups. Second and moreover, the modern plant data reveal that n-alkane chain length distributions are tremendously variable within large vascular plant groups--both functional groups such as woody plants or graminoids as well as phylogenetic groups at the family level or higher. This variability makes it difficult at best to use n-alkane chain lengths to distinguish one vascular group from another, as was previously suggested. Instead, our results suggest that chain length distributions and ACL are driven more by climate, especially temperature. Longer chain lengths, with their increased hydrophobicity, would likely experience favorable selection under warmer or drier conditions where leaf water loss is likely to be a greater stress. Thus, it may be that we can interpret the increase in ACL during the PETM as a direct response by the flora to increased temperature during the hyperthermal event, and n-alkane chain length distributions, properly constrained, may possibly serve as a qualitative paleotemperature proxy.

Probing the Differential Tissue Distribution and Bioaccumulation Behavior of Per- and Polyfluoroalkyl Substances of Varying Chain-Lengths, Isomeric Structures and Functional Groups in Crucian Carp.

PubMed

Shi, Yali; Vestergren, Robin; Nost, Therese Haugdahl; Zhou, Zhen; Cai, Yaqi

2018-04-17

Understanding the bioaccumulation mechanisms of per- and polyfluoroalkyl substances (PFASs) across different chain-lengths, isomers and functional groups represents a monumental scientific challenge with implications for chemical regulation. Here, we investigate how the differential tissue distribution and bioaccumulation behavior of 25 PFASs in crucian carp from two field sites impacted by point sources can provide information about the processes governing uptake, distribution and elimination of PFASs. Median tissue/blood ratios (TBRs) were consistently <1 for all PFASs and tissues except bile which displayed a distinct distribution pattern and enrichment of several perfluoroalkyl sulfonic acids. Transformation of concentration data into relative body burdens (RBBs) demonstrated that blood, gonads, and muscle together accounted for >90% of the amount of PFASs in the organism. Principal component analyses of TBRs and RBBs showed that the functional group was a relatively more important predictor of internal distribution than chain-length for PFASs. Whole body bioaccumulation factors (BAFs) for short-chain PFASs deviated from the positive relationship with hydrophobicity observed for longer-chain homologues. Overall, our results suggest that TBR, RBB, and BAF patterns were most consistent with protein binding mechanisms although partitioning to phospholipids may contribute to the accumulation of long-chain PFASs in specific tissues.

Hydrophobic Tail Length, Degree of Fluorination and Headgroup Stereochemistry are Determinants of the Biocompatibility of (Fluorinated) Carbohydrate Surfactants

PubMed Central

Li, Xueshu; Turánek, Jaroslav; Knötigová, Pavlína; Kudláčková, Hana; Mašek, Josef; Parkin, Sean; Rankin, Stephen E; Knutson, Barbara L; Lehmler, Hans-Joachim

2009-01-01

A series of hydrocarbon and fluorocarbon carbohydrate surfactants with different headgroups (i.e., gluco-, galacto- and maltopyranoside) and (fluorinated) alkyl tails (i.e., C7 and C14 to C19) was synthesized to investigate trends in their cytotoxicity and haemolytic activity, and how surfactant-lipid interactions of selected surfactants contribute to these two measures of biocompatibility. All surfactants displayed low cytotoxicity (EC50 = 25 to > 250 μM) and low haemolytic activity (EC50 = 0.2 to > 3.3 mM), with headgroup structure, tail length and degree of fluorination being important structural determinants for both endpoints. The EC50 values of hydrocarbon and fluorocarbon glucopyranoside surfactants displayed a “cut-off” effect (i.e., a maximum with respect to the chain length). According to steady-state fluorescence anisotropy studies, short chain (C7) surfactants partitioned less readily into model membranes, which explains their low cytotoxicity and haemolytic activity. Interestingly, galactopyranosides were less toxic compared to glucopyranosides with the same hydrophobic tail. Although both surfactant types only differ in the stereochemistry of the 4-OH group, hexadecyl gluco- and galactopyranoside surfactants had similar apparent membrane partition coefficients, but differed in their overall effect on the phase behaviour of DPPC model membranes, as assessed using steady-state fluorescence anisotropy studies. These observations suggest that highly selective surfactant-lipid interactions may be responsible for the differential cytotoxicity and, possible, haemolytic activity of hydrocarbon and fluorocarbon carbohydrate surfactants intended for a variety of pharmaceutical and biomedical applications. PMID:19481909

Evaporation and Hydrocarbon Chain Conformation of Surface Lipid Films.

PubMed

Sledge, Samiyyah M; Khimji, Hussain; Borchman, Douglas; Oliver, Alexandria L; Michael, Heidi; Dennis, Emily K; Gerlach, Dylan; Bhola, Rahul; Stephen, Elsa

2016-10-01

The inhibition of the rate of evaporation (R evap ) by surface lipids is relevant to reservoirs and dry eye. Our aim was to test the idea that lipid surface films inhibit R evap . R evap were determined gravimetrically. Hydrocarbon chain conformation and structure were measured using a Raman microscope. Six 1-hydroxyl hydrocarbons (11-24 carbons in length) and human meibum were studied. Reflex tears were obtained from a 62-year-old male. The Raman scattering intensity of the lipid film deviated by about 7 % for hydroxyl lipids and varied by 21 % for meibum films across the entire film at a resolution of 5 μm 2 . All of the surface lipids were ordered. R evap of the shorter chain hydroxyl lipids were slightly (7%) but significantly lower compared with the longer chain hydroxyl lipids. R evap of both groups was essentially similar to that of buffer. A hydroxyl lipid film did not influence R evap over an estimated average thickness range of 0.69 to >6.9 μm. R evap of human tears and buffer with and without human meibum (34.4 μm thick) was not significantly different. R evap of human tears was not significantly different from buffer. Human meibum and hydroxyl lipids, regardless of their fluidity, chain length, or thickness did not inhibit R evap of buffer or tears even though they completely covered the surface. It is unlikely that hydroxyl lipids can be used to inhibit R evap of reservoirs. Our data do not support the widely accepted (yet unconfirmed) idea that the tear film lipid layer inhibits R evap of tears. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular simulation of dispersion and mechanical stability of organically modified layered silicates in polymer matrices

NASA Astrophysics Data System (ADS)

Fu, Yao-Tsung

The experimental analysis of nanometer-scale separation processes and mechanical properties at buried interfaces in nanocomposites has remained difficult. We have employed molecular dynamics simulation in relation to available experimental data to alleviate such limitations and gain insight into the dispersion and mechanical stability of organically modified layered silicates in hydrophobic polymer matrices. We analyzed cleavage energies of various organically modified silicates as a function of the cation exchange capacity, surfactant head group chemistry, and chain length using MD simulations with the PCFF-PHYLLOSILICATE force field. The range of the cleavage energy is between 25 and 210 mJ/m2 upon the molecular structures and packing of surfactants. As a function of chain length, the cleavage energy indicates local minima for interlayer structures comprised of loosely packed layers of alkyl chains and local maxima for interlayer structures comprised of densely packed layers of alkyl chains between the layers. In addition, the distribution of cationic head groups between the layers in the equilibrium state determines whether large increases in cleavage energy due to Coulomb attraction. We have also examined mechanical bending and failure mechanisms of layered silicates on the nanometer scale using molecular dynamics simulation in comparison to a library of TEM data of polymer nanocomposites. We investigated the energy of single clay lamellae as a function of bending radius and different cation density. The layer energy increases particularly for bending radii below 20 nm and is largely independent of cation exchange capacity. The analysis of TEM images of agglomerated and exfoliated aluminosilicates of different CEC in polymer matrices at small volume fractions showed bending radii in excess of 100 nm due to free volumes in the polymer matrix. At a volume fraction >5%, however, bent clay layers were found with bending radii <20 nm and kinks as a failure mechanism in good agreement with simulation results. We have examined thermal conductivity of organically modified layered silicates using molecular dynamics simulation in comparison to experimental results by laser measurement. The thermal conductivity slightly increased from 0.08 to 0.14 Wm-1K-1 with increasing chain length, related to the gallery spacing and interlayer density of the organic material.

Branched polyesters based on poly[vinyl-3-(dialkylamino)alkylcarbamate-co-vinyl acetate-co-vinyl alcohol]-graft-poly(D,L-lactide-co-glycolide): effects of polymer structure on in vitro degradation behaviour.

PubMed

Unger, Florian; Wittmar, Matthias; Morell, Frank; Kissel, Thomas

2008-05-01

Branched polyesters of the general structure poly[vinyl-3-(dialkylamino)alkylcarbamate-co-vinyl acetate-co-vinyl alcohol]-graft-poly(D,L-lactide-co-glycolide) have shown potential for nano- and micro-scale drug delivery systems. Here the in vitro degradation behaviour with a special emphasis on elucidating structure-property relationships is reported. Effects of type and degree of amine substitution as well as PLGA side chain length were considered. In a first set of experiment, the weight loss of solvent cast films of defined size from 19 polymers was measured as a function of incubation in phosphate buffer (pH 7.4) at 37 degrees C over a time of 21 days. A second study was initiated focusing on three selected polymers in a similar set up, but with additional observation of pH influences (pH 2 and pH 9) and determination of water uptake (swelling) and molecular weights during degradation. Scanning electron micrographs have been recorded at selected time points to characterize film specimens morphologically after degradation. Our investigations revealed the potential to influence the degradation of this polymer class by the degree of amine substitution, higher degrees leading to faster erosion. The erosion rate could further be influenced by the type of amine functionality, DEAPA-modified polyesters degrading as fast as or slightly faster than DMAPA-modified polyesters and these degrading faster than DEAEA-PVA-g-PLGA. As a third option the degradation rate could be modified by the PLGA side chain length, shorter side chains leading to faster erosion. As compared to linear PLGA, remarkably shorter degradation times could be achieved by grafting short PLGA side chains onto amine-modified PVA backbones. Erosion times from less than 5 days to more than 4 weeks could be realized by selecting the type of amine functionality, the degree of amine substitution and the PLGA side chain length at the time of synthesis. In addition, the pathway of hydrolytic degradation can be tuned to be either mainly bulk or surface erosion.

Impact of fatty acyl composition and quantity of triglycerides on bioaccessibility of dietary carotenoids.

PubMed

Huo, Tianyao; Ferruzzi, Mario G; Schwartz, Steven J; Failla, Mark L

2007-10-31

A carotenoid-rich salad meal with varying amounts and types of triglycerides (TG) was digested using simulated gastric and small intestinal conditions. Xanthophylls (lutein and zeaxanthin) and carotenes (alpha-carotene, beta-carotene, and lycopene) in chyme and micelle fraction were quantified to determine digestive stability and efficiency of micellarization (bioaccessibility). Micellarization of lutein (+zeaxanthin) exceeded that of alpha- and beta-carotenes, which was greater than that of lycopene for all test conditions. Micellarization of carotenes, but not lutein (+zeaxanthin), was enhanced (P < 0.05) by addition of TG (2.5% v/w) to the meal and was dependent on fatty acyl chain length in structured TG (c18:1 > c8:0 > c4:0). The degree of unsaturation of c18 fatty acyl chains in TG added to the salad purée did not significantly alter the efficiency of micellarization of carotenoids. Relatively low amounts of triolein and canola oil (0.5-1%) were required for maximum micellarization of carotenes, but more oil (approximately 2.5%) was required when TG with medium chain saturated fatty acyl groups (e.g., trioctanoin and coconut oil) was added to the salad. Uptake of lutein and beta-carotene by Caco-2 cells also was examined by exposing cells to micelles generated during the simulated digestion of salad purée with either triolein or trioctanoin. Cell accumulation of beta-carotene was independent of fatty acyl composition of micelles, whereas lutein uptake was slightly, but significantly, increased from samples with digested triolein compared to trioctanoin. The results show that the in vitro transfer of alpha-carotene, beta-carotene, and lycopene from chyme to mixed micelles during digestion requires minimal (0.5-1%) lipid content in the meal and is affected by the length of fatty acyl chains but not the degree of unsaturation in TG. In contrast, fatty acyl chain length has limited if any impact on carotenoid uptake by small intestinal epithelial cells. These data suggest that the amount of TG in a typical meal does not limit the bioaccessibility of carotenoids.

Phase behavior of stratum corneum lipids in mixed Langmuir-Blodgett monolayers.

PubMed Central

ten Grotenhuis, E; Demel, R A; Ponec, M; Boer, D R; van Miltenburg, J C; Bouwstra, J A

1996-01-01

The lipids found in the bilayers of the stratum corneum fulfill the vital barrier role of mammalian bodies. The main classes of lipids found in stratum corneum are ceramides, cholesterol, and free fatty acids. For an investigation of their phase behavior, mixed Langmuir-Blodgett monolayers of these lipids were prepared. Atomic force microscopy was used to investigate the structure of the monolayers as a function of the monolayer composition. Three different types of ceramide were used: ceramide extracted from pigskin, a commercially available ceramide with several fatty acid chain lengths, and two synthetic ceramides that have only one fatty acid chain length. In pigskin ceramide-cholesterol mixed monolayers phase separation was observed. This phase separation was also found for the commercially available type III Sigma ceramide-cholesterol mixed monolayers with molar ratios ranging from 1:0.1 to 1:1. These monolayers separated into two phases, one composed of the long fatty acid chain fraction of Sigma ceramide III and the other of the short fatty acid chain fraction of Sigma ceramide III mixed with cholesterol. Mixtures with a higher cholesterol content consisted of only one phase. These observations were confirmed by the results obtained with synthetic ceramides, which have only one fatty acid chain length. The synthetic ceramide with a palmitic acid (16:0) chain mixed with cholesterol, and the synthetic ceramide with a lignoceric acid (24:0) chain did not. Free fatty acids showed a preference to mix with one of these phases, depending on their fatty acid chain lengths. The results of this investigation suggest that the model system used in this study is in good agreement with those of other studies concerning the phase behavior of the stratum corneum lipids. By varying the composition of the monolayers one can study the role of each lipid class in detail. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 PMID:8874014

Driven translocation of Polymer through a nanopore: effect of heterogeneous flexibility

NASA Astrophysics Data System (ADS)

Adhikari, Ramesh; Bhattacharya, Aniket

2014-03-01

We have studied translocation of a model bead-spring polymer through a nanopore whose building blocks consist of alternate stiff and flexible segments and variable elastic bond potentials. For the case of uniform spring potential translocation of a symmetric periodic stiff-flexible chain of contour length N and segment length m (mod(N,2m)=0), we find that the end-to-end distance and the mean first passage time (MFPT) have weak dependence on the length m. The characteristic periodic pattern of the waiting time distribution captures the stiff and flexible segments of the chain with stiff segments taking longer time to translocate. But when we vary both the elastic bond energy, and the bending energy, as well as the length of stiff/flexible segments, we discover novel patterns in the waiting time distribution which brings out structural information of the building blocks of the translocating chain. Partially supported by UCF Office of Research and Commercialization & College of Science SEED grant.

Determination of the thermal stability of perfluoroalkylethers

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1990-01-01

The thermal decomposition temperatures of several commercial and custom synthesized perfluoroalkylether fluids were determined with a computerized tensimeter. In general, the decomposition temperatures of the commercial fluids were all similar and significantly higher than those for custom synthesized fluids. Correlation of the decomposition temperatures with the molecular structures of the primary components of the commercial fluids revealed that the stability of the fluids is not affected by intrinsic factors such as carbon chain length, branching, or cumulated difluoroformal groups. Instead, correlation with extrinsic factors revealed that the stability may be limited by the presence of small quantities of thermally unstable material and/or chlorine-containing material arising from the use of chlorine-containing solvents during synthesis. Finally, correlation of decomposition temperatures with molecular weights for Demnum and Krytox fluids supports a chain cleavage reaction mechanism for Demnum fluids and an unzipping reaction mechanism for Krytox fluids.

Control of DNA-Functionalized Nanoparticle Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries, and drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, as well as the parameters to develop colloidal models that reproduce both the shape of single crystals and their growth kinetics.

Effect of suppression of arabinoxylan synthetic genes in wheat endosperm on chain length of arabinoxylan and extract viscosity.

PubMed

Freeman, Jackie; Lovegrove, Alison; Wilkinson, Mark David; Saulnier, Luc; Shewry, Peter Robert; Mitchell, Rowan Andrew Craig

2016-01-01

Arabinoxylan (AX) is the dominant component within wheat (Triticum aestivum L.) endosperm cell walls, accounting for 70% of the polysaccharide. The viscosity of aqueous extracts from wheat grain is a key trait influencing the processing for various end uses, and this is largely determined by the properties of endosperm AX. We have previously shown dramatic effects on endosperm AX in transgenic wheat by down-regulating either TaGT43_2 or TaGT47_2 genes (orthologues to IRX9 and IRX10 in Arabidopsis, respectively) implicated in AX chain extension and the TaXAT1 gene responsible for monosubstitution by 3-linked arabinose. Here, we use these transgenic lines to investigate the relationship between amounts of AX in soluble and insoluble fractions, the chain-length distribution of these measured by intrinsic viscosity and the overall effect on extract viscosity. In transgenic lines expressing either the TaGT43_2 or TaGT47_2 RNAi transgenes, the intrinsic viscosities of water-extractable (WE-AX) and of a water-insoluble alkaline-extracted fraction (AE-AX) were decreased by between 10% and 50% compared to control lines. In TaXAT1 RNAi lines, there was a 15% decrease in intrinsic viscosity of WE-AX but no consistent effect on that of AE-AX. All transgenic lines showed decreases in extract viscosity with larger effects in TaGT43_2 and TaGT47_2 RNAi lines (by up to sixfold) than in TaXAT1 RNAi lines (by twofold). These effects were explained by the decreases in amount and chain length of WE-AX, with decreases in amount having the greater influence. Extract viscosity from wheat grain can therefore be greatly decreased by suppression of single gene targets. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Two Predicted Transmembrane Domains Exclude Very Long Chain Fatty acyl-CoAs from the Active Site of Mouse Wax Synthase

PubMed Central

Kawelke, Steffen; Feussner, Ivo

2015-01-01

Wax esters are used as coatings or storage lipids in all kingdoms of life. They are synthesized from a fatty alcohol and an acyl-CoA by wax synthases. In order to get insights into the structure-function relationships of a wax synthase from Mus musculus, a domain swap experiment between the mouse acyl-CoA:wax alcohol acyltransferase (AWAT2) and the homologous mouse acyl-CoA:diacylglycerol O-acyltransferase 2 (DGAT2) was performed. This showed that the substrate specificity of AWAT2 is partially determined by two predicted transmembrane domains near the amino terminus of AWAT2. Upon exchange of the two domains for the respective part of DGAT2, the resulting chimeric enzyme was capable of incorporating up to 20% of very long acyl chains in the wax esters upon expression in S. cerevisiae strain H1246. The amount of very long acyl chains in wax esters synthesized by wild type AWAT2 was negligible. The effect was narrowed down to a single amino acid position within one of the predicted membrane domains, the AWAT2 N36R variant. Taken together, we provide first evidence that two predicted transmembrane domains in AWAT2 are involved in determining its acyl chain length specificity. PMID:26714272

Structure of Waxy Maize Starch Hydrolyzed by Maltogenic α-Amylase in Relation to Its Retrogradation.

PubMed

Grewal, Navneet; Faubion, Jon; Feng, Guohua; Kaufman, Rhett C; Wilson, Jeff D; Shi, Yong-Cheng

2015-04-29

Maltogenic α-amylase is widely used as an antistaling agent in bakery foods. The objective of this study was to determine the degree of hydrolysis (DH) and starch structure after maltogenic amylase treatments in relation to its retrogradation. Waxy maize starch was cooked and hydrolyzed to different degrees by a maltogenic amylase. High-performance anion-exchange chromatography and size exclusion chromatography were used to determine saccharides formed and the molecular weight (Mw) distributions of the residual starch structure, respectively. Chain length (CL) distributions of debranched starch samples were further related to amylopectin (AP) retrogradation. Differential scanning calorimetry (DSC) results showed the complete inhibition of retrogradation when starches were hydrolyzed to >20% DH. Mw and CL distributions of residual AP structure indicated that with an increase in %DH, a higher proportion of unit chains with degree of polymerization (DP) ≤9 and a lower proportion of unit chains with DP ≥17 were formed. A higher proportion of short outer AP chains that cannot participate in the formation of double helices supports the decrease in and eventual inhibition of retrogradation observed with the increase in %DH. These results suggest that the maltogenic amylase could play a powerful role in inhibiting the staling of baked products even at limited starch hydrolysis.

Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination.

PubMed

Savidor, Alon; Barzilay, Rotem; Elinger, Dalia; Yarden, Yosef; Lindzen, Moshit; Gabashvili, Alexandra; Adiv Tal, Ophir; Levin, Yishai

2017-06-01

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Removal efficiency of multiple poly- and perfluoroalkyl substances (PFASs) in drinking water using granular activated carbon (GAC) and anion exchange (AE) column tests.

PubMed

McCleaf, Philip; Englund, Sophie; Östlund, Anna; Lindegren, Klara; Wiberg, Karin; Ahrens, Lutz

2017-09-01

Poly- and perfluoroalkyl substances (PFASs) have been detected in drinking water at relatively high concentrations throughout the world which has led to implementation of regulatory guidelines for specific PFASs in drinking water in several European countries and in the U.S. The Swedish National Food Agency has determined that the drinking water of over one third of the country's municipal consumers is at risk or already affected by PFAS contamination. The present study investigated the effects of perfluorocarbon chain length, functional group and isomer structure (branched or linear) on removal of multiple PFASs using granular activated carbon (GAC, Filtrasorb ® 400) and anion exchange (AE, Purolite ® A600) column experiments. The removal of 14 different PFASs, i.e. the C 3 C 11 , C 14 perfluoroalkyl carboxylic acids (PFCAs) (PFBA, PFPeA, PFHxA, PFHpA, PFOA, PFNA, PFDA, PFUnDA, PFDoDA, PFTeDA), perfluorooctane sulfonamide (FOSA), and the C 4 , C 6 , C 8 perfluoroalkyl sulfonic acids (PFSAs) (PFBS, PFHxS, PFOS), was monitored for a 217 day period. The results indicate the selective nature of PFAS removal as the absorbents are loaded with PFASs and dissolved organic carbon (DOC). A clear relationship between perfluorocarbon chain length and removal efficiency of PFASs using GAC and AE was found while PFASs with sulfonate functional groups displayed greater removal efficiency than those with carboxylate groups. Similarly, time to column breakthrough increased with increasing perfluorocarbon chain length and was greater for the PFSAs than the PFCAs for both GAC and AE. Shorter carbon chained PFASs such as PFBA, PFPeA, PFHxA showed desorption behavior and long-chained PFASs showed increased removal towards the end of the experiment indicating agglomeration or micelle development. Linear isomers of PFOS, PFHxS, and perfluorooctane sulfonamide (FOSA) had greater column removal efficiencies using GAC (and also for AE at greater bed volume throughput) than the branched and this difference increased at greater bed volume throughputs. The GAC and AE columns showed a poor correlation between DOC and PFAS removal efficiency. The results indicate that designers and operators of AE and GAC treatment processes must take into consideration the selective nature of PFAS removal and associated desorption of short-chain PFCAs during co-removal of multiple PFASs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of hyaluronan chain length in buffering interstitial flow across synovium in rabbits

PubMed Central

Coleman, P J; Scott, D; Mason, R M; Levick, J R

2000-01-01

Synovial fluid drains out of joints through an interstitial pathway. Hyaluronan, the major polysaccharide of synovial fluid, attenuates this fluid drainage; it creates a graded opposition to outflow that increases with pressure (outflow ‘buffering’). This has been attributed to size-related molecular reflection at the interstitium-fluid interface. Chain length is reduced in inflammatory arthritis. We therefore investigated the dependence of outflow buffering on hyaluronan chain length.Hyaluronan molecules of mean molecular mass ≈2200, 530, 300 and 90 kDa and concentration 3.6 mg ml−1 were infused into the knees of anaesthetized rabbits, with Ringer solution as control in the contralateral joint. Trans-synovial drainage rate was recorded at known joint pressures. Pressure was raised in steps every 30–60 min (range 2–24 cmH2O).With hyaluronan-90 and hyaluronan-300 the fluid drainage rate was reduced relative to Ringer solution (P < 0.001, ANOVA) but increased steeply with pressure. The opposition to outflow, defined as the pressure required to drive unit outflow, did not increase with pressure, i.e. there was no outflow buffering.With hyaluronan-530 and hyaluronan-2000 the fluid drainage rate became relatively insensitive to pressure, causing a near plateau of flow. Opposition to outflow increased markedly with pressure, by up to 3.3 times over the explored pressures.Hyaluronan concentration in the joint cavity increased over the drainage period, indicating partial reflection of hyaluronan by synovial interstitium. Reflected fractions were 0.12, 0.33, 0.25 and 0.79 for hyaluronan-90, -300, -530 and -2200, respectively.Thus the flow-buffering effect of hyaluronan depended on chain length, and shortening the chains reduced the degree of molecular reflection. The latter should reduce the concentration polarization at the tissue interface, and hence the local osmotic pressure opposing fluid drainage. In rheumatoid arthritis the reduced chain length will facilitate the escape of hyaluronan and fluid. PMID:10896731

Influence of acid chain length on the properties of TiO2 prepared by sol-gel method and LC-MS studies of methylene blue photodegradation.

PubMed

Bakre, Pratibha V; Volvoikar, Prajesh S; Vernekar, Amit A; Tilve, S G

2016-07-15

Nano-sized titanium dioxide photocatalysts were synthesized by hybrid hydrolytic nonhydrolytic sol-gel method using aliphatic organic acid templates to study the effect of chain length on their properties. X-ray diffraction pattern indicated crystalline anatase phase. The Barrett-Joyner-Halenda surface area measurement gave surface area ranging from 98.4 to 205.5m(2)/g and was found to be dependent on the chain length of the aliphatic acid. The longer chain acids rendered the material with high surface area. The organic acids acted as bidentate ligand and a surfactant in controlling the size and the mesoporosity. The size of the TiO2 nanoparticulate was found to be in the range of 10-18nm. The catalyst prepared by employing long chain acids octanoic acid and palmitic acid had smaller size, narrow pore radius, higher surface area and showed better photocatalytic activity than the commercially available Degussa P25 catalyst for the degradation of methylene blue dye. A new intermediate was identified by tandem liquid chromatography mass spectrometry studies during the degradation of methylene blue solution. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

NASA Astrophysics Data System (ADS)

Putra, Edy Giri Rachman; Patriati, Arum

2015-04-01

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2-10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30-50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol, octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.

Is the liquid or the solid phase responsible for the low melting points of ionic liquids? Alkyl-chain-length dependence of thermodynamic properties of [C nmim][Tf 2N

NASA Astrophysics Data System (ADS)

Shimizu, Yoshitaka; Ohte, Yoko; Yamamura, Yasuhisa; Saito, Kazuya

2009-03-01

To establish the alkyl-chain-length dependences of thermodynamic properties of typical ionic liquids [C nmim][Tf 2N], the heat capacities of compounds with n = 2 and 18 were measured by adiabatic calorimetry. The comparison with other ionic liquids and typical molecular substances reveals that the low melting point of [C nmim][Tf 2N] with a short alkyl chain mainly originate in the large fusion entropy arising from the low entropy of the crystalline phase.

Pulsed flows, tributary inputs, and food web structure in a highly regulated river

USGS Publications Warehouse

Sabo, John; Caron, Melanie; Doucett, Richard R.; Dibble, Kimberly L.; Ruhi, Albert; Marks, Jane; Hungate, Bruce; Kennedy, Theodore A.

2018-01-01

1.Dams disrupt the river continuum, altering hydrology, biodiversity, and energy flow. Although research indicates that tributary inputs have the potential to dilute these effects, knowledge at the food web level is still scarce.2.Here we examined the riverine food web structure of the Colorado River below Glen Canyon Dam, focusing on organic matter sources, trophic diversity, and food chain length. We asked how these components respond to pulsed flows from tributaries following monsoon thunderstorms that seasonally increase streamflow in the American Southwest.3.Tributaries increased the relative importance of terrestrial organic matter, particularly during the wet season below junctures of key tributaries. This contrasted with the algal-based food web present immediately below Glen Canyon Dam.4.Tributary inputs during the monsoon also increased trophic diversity and food chain length: food chain length peaked below the confluence with the largest tributary (by discharge) in Grand Canyon, increasing by >1 trophic level over a 4-5 kilometre reach possibly due to aquatic prey being flushed into the mainstem during heavy rain events.5.Our results illustrate that large tributaries can create seasonal discontinuities, influencing riverine food web structure in terms of allochthony, food web diversity, and food chain length.6.Synthesis and applications. Pulsed flows from unregulated tributaries following seasonal monsoon rains increase the importance of terrestrially-derived organic matter in large, regulated river food webs, increasing food chain length and trophic diversity downstream of tributary inputs. Protecting unregulated tributaries within hydropower cascades may be important if we are to mitigate food web structure alteration due to flow regulation by large dams. This is critical in the light of global hydropower development, especially in megadiverse, developing countries where dam placement (including completed and planned structures) is in tributaries.

Fundamental Characterization of the Micellar Self-Assembly of Sophorolipid Esters.

PubMed

Koh, Amanda; Todd, Katherine; Sherbourne, Ezekiel; Gross, Richard A

2017-06-13

Surfactants are ubiquitous constituents of commercial and biological systems that function based on complex structure-dependent interactions. Sophorolipid (SL) n-alkyl esters (SL-esters) comprise a group of modified naturally derived glycolipids from Candida bombicola. Herein, micellar self-assembly behavior as a function of SL-ester chain length was studied. Surface tensions as low as 31.2 mN/m and critical micelle concentrations (CMCs) as low as 1.1 μM were attained for diacetylated SL-decyl ester (dASL-DE) and SL-octyl ester, respectively. For deacetylated SL-esters, CMC values reach a lower limit at SL-ester chains above n-butyl (SL-BE, 1-3 μM). This behavior of SL-esters with increasing hydrophobic tail length is unlike other known surfactants. Diffusion-ordered spectroscopy (DOSY) and T 1 relaxation NMR experiments indicate this behavior is due to a change in intramolecular interactions, which impedes the self-assembly of SL-esters with chain lengths above SL-BE. This hypothesis is supported by micellar thermodynamics where a disruption in trends occurs at n-alkyl ester chain lengths above those of SL-BE and SL-hexyl ester (SL-HE). Diacetylated (dA) SL-esters exhibit an even more unusual trend in that CMC increases from 1.75 to 815 μM for SL-ester chain lengths of dASL-BE and dASL-DE, respectively. Foaming studies, performed to reveal the macroscopic implications of SL-ester micellar behavior, show that the observed instability in foams formed using SL-esters are due to coalescence, which highlights the importance of understanding intermicellar interactions. This work reveals that SL-esters are an important new family of green high-performing surfactants with unique structure-property relationships that can be tuned to optimize micellar characteristics.

Intercalation of the layered solid acid HCa/sub 2/Nb/sub 3/O/sub 10/ by organic amines

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

Jacobson, A.J.; Johnson, J.W.; Lewandowski, J.T.

1987-01-01

Layered compounds of formula C/sub n/H/sub 2n+1/NH/sub 3/Ca/sub 2/Nb/sub 3/O/sub 10/ are formed by reaction of n-alkylamines with the solid acid HCa/sub 2/Nb/sub 3/O/sub 10/. Other organic bases such as pyridine can also be intercalated. The lattice constants of the new compounds have been determined by powder X-ray diffraction. The unit cells are tetragonal with a axes that are unchanged with variation of the intercalated amine. The c axes lengths (layer spacings) vary systematically with the hydrocarbon chain length of the alkylamine.

[Study on anti-bacterium activity of ginkgolic acids and their momomers].

PubMed

Yang, Xiaoming; Zhu, Wei; Chen, Jun; Qian, Zhiyu; Xie, Jimin

2004-09-01

Ginkgolic acids and their three monomers were separated from ginkgo sarcotestas. The anti-bacterium activity of ginkgolic acids were tested. The relation between the anti-bacterium activity and side chain of ginkgolic acid were studied. The MIC of ginkgolic acids and their three monomers and salicylic acid were tested. Ginkgolic acid has strong inhibitive effect on G+-bacterium. Salicylic acid has no side chain, so no anti-bacterial activity. When the length of gingkolic acid side chain is C13:0, it has the strongest anti-bacterial activity in three monomers. The side chain of ginkgolic acid is the key functional group that possessed anti-bacterial activity. The length of Ginkgolic acid was the main effective factor of anti-bacterial activity.

Initial stages of aggregation in aqueous solutions of ionic liquids: molecular dynamics studies.

PubMed

Bhargava, B L; Klein, Michael L

2009-07-16

Structures formed by 1-alkyl-3-methylimidazolium bromide aqueous solutions with decyl, dodecyl, tetradecyl, and hexadecyl chains have been studied using molecular dynamics (MD) simulations. Spontaneous self-assembly of the amphiphilic cations to form quasi-spherical polydisperse aggregates has been observed in all of the systems, with the size and nature of the aggregates varying with chain length. In all systems, the cation alkyl tails are buried deep inside the aggregates with the polar imidazolium group exposed to exploit the favorable interactions with water. Aggregation numbers steadily increase with the chain length. The hexadecyl aggregates have the most ordered internal structure of the systems studied, and the alkyl chains in these cations show the least number of gauche defects.

Chain Length Dependence of Energies of Electron and Triplet Polarons in Oligofluorenes

DOE PAGES

Chen, Hung Cheng; Sreearunothai, Paiboon; Cook, Andrew R.; ...

2017-03-01

Bimolecular equilibria measured the one-electron reduction potentials and triplet free energies (ΔG° T) of oligo(9,9-dihexyl)fluorenes and a polymer with lengths of n = 1–10 and 57 repeat units. We can accurately measure one-electron potentials electrochemically only for the shorter oligomers. Starting at n = 1 the free energies change rapidly with increasing length and become constant for lengths longer than the delocalization length. Both the reduction potentials and triplet energies can be understood as the sum of a free energy for a fixed polaron and a positional entropy. Furthermore, the positional entropy increases gradually with length beyond the delocalization lengthmore » due to the possible occupation sites of the charge or the triplet exciton. Our results reinforce the view that charges and triplet excitons in conjugated chains exist as polarons and find that positional entropy can replace a popular empirical model of the energetics.« less

Determination of integron frequency by a polymerase chain reaction-restriction fragment length polymorphism method in multidrug-resistant Escherichia coli, which causes urinary tract infections.

PubMed

Fallah, Fatemeh; Karimi, Abdollah; Goudarzi, Mehdi; Shiva, Farideh; Navidinia, Masoumeh; Jahromi, Mana Hadipour; Sajadi Nia, Raheleh Sadat

2012-12-01

The purpose of this study was to determine the presence of integrons in Escherichia coli, which cause urinary tract infections, and to define the association between integrons and antimicrobial susceptibility. Susceptibility of 200 isolates from urine samples of patients suffering from urinary tract infections to 13 antibiotics was determined by the Kirby-Bauer disk diffusion method. The existence of class1 and 2 integrons in resistant isolates was assessed by polymerase chain reaction-restriction fragment length polymorphism and sequencing. Antibiotic resistance patterns were observed as follows: amoxicillin 78%, tetracycline 76.1%, co-trimoxazole 67.7%, cephalotin 60%, nalidixic acid 57.4%, chloramphenicol 49%, gentamicin 46.4%, ceftazidim 38.1%, ciprofloxacin 36.2%, nitrofurantoin 33.5%, amikacin 32.1%, norfloxacin 36.1%, and imipenem 27.1%. Of 200 isolates, 155 (77.5%) were multidrug resistant (MDR). The existence of integrons was confirmed in 50.3% of isolates. Three class 1 integron types, aadA2 being the most frequently found, and four class 2 integron types are described. Significant association between resistance to gentamicin, co-trimoxazole, cephalotin, ceftazidim, imipenem, chloramphenicol, and nalidixic acid with the existence of integrons was observed. Multidrug resistance suggests that the strategy for treatment of patients with E.coli infections needs to be revised. Furthermore, it was shown that integrons may be partly responsible for multidrug resistance. Imipenem and norfloxacin were the most effective antibiotics against isolates.

Crystal Structures of Lys-63-linked tri- and di-ubiquitin Reveal a Highly Extended Chain Architecture

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

Weeks, S.; Grasty, K; Hernandez-Cuebas, L

2009-01-01

The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 {angstrom}, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handedmore » helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of {approx}110 {angstrom}. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.« less

Two-dimensional chromatography of complex polymers, 8. Separation of fatty alcohol ethoxylates simultaneously by end group and chain length.

PubMed

Raust, Jacques-Antoine; Bruell, Adele; Sinha, Pritish; Hiller, Wolf; Pasch, Harald

2010-09-01

A comprehensive two-dimensional liquid chromatography system was developed to precisely describe the molecular heterogeneity of fatty alcohol ethoxylates. The end-group functionality was analyzed by gradient HPLC while ethylene oxide oligomer distributions were characterized by liquid adsorption chromatography. A baseline separation of all functionality fractions irrespective of the ethylene oxide oligomer chain length was achieved on nonpolar X-Terra(®) C(18) with a methanol-water gradient, whereas an isocratic flow of isopropanol-water on a polar Chromolith(®) Si column gave a separation according to the oligomer chain length without interference of the end-group distribution. The combination of these two methods to conduct online two-dimensional liquid chromatography experiments resulted in a comprehensive two-dimensional picture on the molecular heterogeneity of the sample.

Analysis of Medium-Chain-Length Polyhydroxyalkanoate-Producing Bacteria in Activated Sludge Samples Enriched by Aerobic Periodic Feeding.

PubMed

Lee, Sun Hee; Kim, Jae Hee; Chung, Chung-Wook; Kim, Do Young; Rhee, Young Ha

2018-04-01

Analysis of mixed microbial populations responsible for the production of medium-chain-length polyhydroxyalkanoates (MCL-PHAs) under periodic substrate feeding in a sequencing batch reactor (SBR) was conducted. Regardless of activated sludge samples and the different MCL alkanoic acids used as the sole external carbon substrate, denaturing gradient gel electrophoresis analysis indicated that Pseudomonas aeruginosa was the dominant bacterium enriched during the SBR process. Several P. aeruginosa strains were isolated from the enriched activated sludge samples. The isolates were subdivided into two groups, one that produced only MCL-PHAs and another that produced both MCL- and short-chain-length PHAs. The SBR periodic feeding experiments with five representative MCL-PHA-producing Pseudomonas species revealed that P. aeruginosa has an advantage over other species that enables it to become dominant in the bacterial community.

Design of multi-phase dynamic chemical networks

NASA Astrophysics Data System (ADS)

Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-08-01

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

Butyric acid esterification kinetics over Amberlyst solid acid catalysts: the effect of alcohol carbon chain length.

PubMed

Pappu, Venkata K S; Kanyi, Victor; Santhanakrishnan, Arati; Lira, Carl T; Miller, Dennis J

2013-02-01

The liquid phase esterification of butyric acid with a series of linear and branched alcohols is examined. Four strong cation exchange resins, Amberlyst™ 15, Amberlyst™ 36, Amberlyst™ BD 20, and Amberlyst™ 70, were used along with para-toluenesulfonic acid as a homogeneous catalyst. The effect of increasing alcohol carbon chain length and branching on esterification rate at 60°C is presented. For all catalysts, the decrease in turnover frequency (TOF) with increasing carbon chain length of the alcohol is described in terms of steric hindrance, alcohol polarity, and hydroxyl group concentration. The kinetics of butyric acid esterification with 2-ethylhexanol using Amberlyst™ 70 catalyst is described with an activity-based, pseudo-homogeneous kinetic model that includes autocatalysis by butyric acid. Copyright © 2012 Elsevier Ltd. All rights reserved.

Application of the compensated arrhenius formalism to dielectric relaxation.

PubMed

Petrowsky, Matt; Frech, Roger

2009-12-17

The temperature dependence of the dielectric rate constant, defined as the reciprocal of the dielectric relaxation time, is examined for several groups of organic solvents. Early studies of linear alcohols using a simple Arrhenius equation found that the activation energy was dependent on the chain length of the alcohol. This paper re-examines the earlier data using a compensated Arrhenius formalism that assumes the presence of a temperature-dependent static dielectric constant in the exponential prefactor. Scaling temperature-dependent rate constants to isothermal rate constants so that the dielectric constant dependence is removed results in calculated energies of activation E(a) in which there is a small increase with chain length. These energies of activation are very similar to those calculated from ionic conductivity data using compensated Arrhenius formalism. This treatment is then extended to dielectic relaxation data for n-alkyl bromides, n-nitriles, and n-acetates. The exponential prefactor is determined by dividing the temperature-dependent rate constants by the Boltzmann term exp(-E(a)/RT). Plotting the prefactors versus the static dielectric constant places the data on a single master curve for each group of solvents.

Molecular identification of Giardia duodenalis in Ecuador by polymerase chain reaction-restriction fragment length polymorphism

PubMed Central

Atherton, Richard; Bhavnani, Darlene; Calvopiña, Manuel; Vicuña, Yosselin; Cevallos, William; Eisenberg, Joseph

2013-01-01

The aim of this study was to determine the genetic diversity of Giardia duodenalis present in a human population living in a northern Ecuadorian rain forest. All Giardia positive samples (based on an ELISA assay) were analysed using a semi-nested polymerase chain reaction-restriction fragment length polymorphism assay that targets the glutamate dehydrogenase (gdh) gene; those amplified were subsequently genotyped using NlaIV and RsaI enzymes. The gdh gene was successfully amplified in 74 of 154 ELISA positive samples; 69 of the 74 samples were subsequently genotyped. Of these 69 samples, 42 (61%) were classified as assemblage B (26 as BIII and 16 as BIV), 22 (32%) as assemblage A (3 as AI and 19 as AII) and five (7%) as mixed AII and BIII types. In this study site we observe similar diversity in genotypes to other regions in Latin America, though in contrast to some previous studies, we found similar levels of diarrheal symptoms in those individuals infected with assemblage B compared with those infected with assemblage A. PMID:23827993

The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2.

PubMed

León, I; Alonso, E R; Mata, S; Cabezas, C; Rodríguez, M A; Grabow, J-U; Alonso, J L

2017-09-20

The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH 2 ) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy. The rotational and quadrupole coupling constants of the two 14 N nuclei determined in this work show that this dipeptide exists as a mixture of C 7 and C 5 conformers in the supersonic expansion. The conformers are stabilized by a C[double bond, length as m-dash]OH-N intramolecular hydrogen bond closing a seven- or a five-membered ring, respectively. The observation of both conformers is in good agreement with previous results on the related dipeptides containing different residues, confirming that the polarity/non-polarity of the side chains of the amino acid is responsible for the conformational locking/unlocking. The voluminous isopropyl group is not able to prevent the less stable C 5 conformer from forming but it destabilizes the C[double bond, length as m-dash]OH-N interaction.

Brownian dynamics simulation of a polymer chain in a solid-state nanopore attached to a molecular stop

NASA Astrophysics Data System (ADS)

Wells, Craig; Hulings, Zachery; Melnikov, Dmitriy; Gracheva, Maria

We study a nanopore inside a silicon dioxide membrane submerged in a KCl solution with a negatively charged polymer chain of varying lengths whose movement is described using Brownian dynamics. The polymer is attached to a molecule with a radius larger than that of the nanopore's which acts as a molecular stop, allowing the chain to thread the nanopore but preventing it from translocating. We found that the polymer chain's variation of movement along the nanopore decreased when increasing applied biases and chain lengths for portions of the chain closest to the molecular stop. The chain displacement within the pore is also compared to a freely translocating polymer where preliminary results show the free polymer having a greater variation in the radial direction. Overall, our preliminary results indicate that the radial direction of the polymer chain is dominated by the confinement in the narrow nanopore with restrictions imposed by the molecular stop and bias playing a lesser role. Understanding the interaction behavior of the polymer chain-stop molecule may lead to methods that decrease movement variation, facilitating an improvement on characterizing and identification of molecules. NSF DMR and CBET Grant No. 1352218.

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

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

Nagayama, Gyoko, E-mail: nagayama@mech.kyutech.ac.jp; Takematsu, Masaki; Mizuguchi, Hirotaka

2015-07-07

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

Electrostatic persistence length.

PubMed

Fixman, Marshall

2010-03-11

The persistence length is calculated for polyelectrolyte chains with fixed bond lengths and bond angles (pi-theta), and a potential energy consisting of the screened Coulomb interaction between beads, potential wells alpha phi(i)2 for the dihedral angles phi(i), and coupling terms beta phi(i) phi(i+/-1). This model defines a librating chain that reduces in appropriate limits to the freely rotating or wormlike chains, it can accommodate local crumpling or extreme stiffness, and it is easy to simulate. A planar-quadratic (pq), analytic approximation is based on an expansion of the electrostatic energy in eigenfunctions of the quadratic form that describes the backbone energy, and on the assumption that the quadratic form not only is positive but also adequately confines the chain in an infinite phase space of dihedral angles to the physically unique part with all |phi(i)| < pi. The pq approximation is available under these weak constraints, but the simulations confirm its quantitative accuracy only under the expected condition that alpha is large, that is, for very stiff chains. Stiff chains can also be simulated with small alpha and small theta and compared to an OSF approximation suitably generalized to chains with finite rather than vanishing theta, and increasing agreement with OSF is found the smaller is theta. The two approximations, one becoming exact as alpha --> infinity with fixed theta, the other as theta --> 0 with fixed alpha, are quantitatively similar in behavior, both giving a persistence length P = P0 + aD2 for stiff chains, where D is the Debye length. However, the coefficient apq is about twice the value of aOSF. Under other conditions the simulations show that P may or not be linear in D2 at small or moderate D, depending on the magnitudes of alpha, beta, theta, and the charge density but always becomes linear at large D. Even at a moderately low charge density, corresponding to fewer than 20% of the beads being charged, and with strong crumpling induced by large beta, increasing D dissolves blobs and recovers a linear dependence of P on D2, although a lower power of D gives an adequate fit at moderate D. For the class of models considered, it is concluded that the only universal feature is the asymptotic linearity of P in D2, regardless of flexibility or stiffness.

Kondo length in bosonic lattices

NASA Astrophysics Data System (ADS)

Giuliano, Domenico; Sodano, Pasquale; Trombettoni, Andrea

2017-09-01

Motivated by the fact that the low-energy properties of the Kondo model can be effectively simulated in spin chains, we study the realization of the effect with bond impurities in ultracold bosonic lattices at half filling. After presenting a discussion of the effective theory and of the mapping of the bosonic chain onto a lattice spin Hamiltonian, we provide estimates for the Kondo length as a function of the parameters of the bosonic model. We point out that the Kondo length can be extracted from the integrated real-space correlation functions, which are experimentally accessible quantities in experiments with cold atoms.

Draft Genome Sequence of Pseudomonas sp. Strain LFM046, a Producer of Medium-Chain-Length Polyhydroxyalkanoate.

PubMed

Cardinali-Rezende, Juliana; Alexandrino, Paulo Moises Raduan; Nahat, Rafael Augusto Theodoro Pereira de Souza; Sant'Ana, Débora Parrine Vieira; Silva, Luiziana Ferreira; Gomez, José Gregório Cabrera; Taciro, Marilda Keico

2015-08-20

Pseudomonas sp. LFM046 is a medium-chain-length polyhydroxyalkanoate (PHAMCL) producer capable of using various carbon sources (carbohydrates, organic acids, and vegetable oils) and was first isolated from sugarcane cultivation soil in Brazil. The genome sequence was found to be 5.97 Mb long with a G+C content of 66%. Copyright © 2015 Cardinali-Rezende et al.

Abnormal glycogen chain length pattern, not hyperphosphorylation, is critical in Lafora disease.

PubMed

Nitschke, Felix; Sullivan, Mitchell A; Wang, Peixiang; Zhao, Xiaochu; Chown, Erin E; Perri, Ami M; Israelian, Lori; Juana-López, Lucia; Bovolenta, Paola; Rodríguez de Córdoba, Santiago; Steup, Martin; Minassian, Berge A

2017-07-01

Lafora disease (LD) is a fatal progressive epilepsy essentially caused by loss-of-function mutations in the glycogen phosphatase laforin or the ubiquitin E3 ligase malin. Glycogen in LD is hyperphosphorylated and poorly hydrosoluble. It precipitates and accumulates into neurotoxic Lafora bodies (LBs). The leading LD hypothesis that hyperphosphorylation causes the insolubility was recently challenged by the observation that phosphatase-inactive laforin rescues the laforin-deficient LD mouse model, apparently through correction of a general autophagy impairment. We were for the first time able to quantify brain glycogen phosphate. We also measured glycogen content and chain lengths, LBs, and autophagy markers in several laforin- or malin-deficient mouse lines expressing phosphatase-inactive laforin. We find that: (i) in laforin-deficient mice, phosphatase-inactive laforin corrects glycogen chain lengths, and not hyperphosphorylation, which leads to correction of glycogen amounts and prevention of LBs; (ii) in malin-deficient mice, phosphatase-inactive laforin confers no correction; (iii) general impairment of autophagy is not necessary in LD We conclude that laforin's principle function is to control glycogen chain lengths, in a malin-dependent fashion, and that loss of this control underlies LD. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Spacer length controlled lamello-columnar to oblique-columnar mesophase transition in liquid crystalline DNA - discotic cationic lipid complexes

NASA Astrophysics Data System (ADS)

Zhu, Lei; Cui, Li; Miao, Jianjun

2006-03-01

A series of asymmetric triphenylene imidazolium salts with different spacer lengths (C5, C8, and C11) were synthesized and their ionic complexes with double-strand DNA were prepared in aqueous solution. The molecular composition of the complexes was determined by FTIR analysis. The liquid crystalline morphology was characterized by polarized light microscopy, X-ray diffraction (XRD), and transmission electron microscope. 2D XRD results indicated an oblique columnar phase for the complex with a short spacer length of C5, while lamello-columnar phases for those with longer spacer lengths (C8 and C11). Thin film circular dichroism results showed the disappearing of any helical conformation in the DNA in all the complexes. Instead, the complexation between single-strand RNA and discotic cationic lipids did not show columnar morphology; therefore, the columnar liquid crystalline morphology in the DNA-discotic cationic lipid complexes was attributed to the DNA double-strand chain rigidity.

Colloidal and antibacterial properties of novel triple-headed, double-tailed amphiphiles: exploring structure-activity relationships and synergistic mixtures.

PubMed

Marafino, John N; Gallagher, Tara M; Barragan, Jhosdyn; Volkers, Brandi L; LaDow, Jade E; Bonifer, Kyle; Fitzgerald, Gabriel; Floyd, Jason L; McKenna, Kristin; Minahan, Nicholas T; Walsh, Brenna; Seifert, Kyle; Caran, Kevin L

2015-07-01

Two novel series of tris-cationic, tripled-headed, double-tailed amphiphiles were synthesized and the effects of tail length and head group composition on the critical aggregation concentration (CAC), thermodynamic parameters, and minimum inhibitory concentration (MIC) against six bacterial strains were investigated. Synergistic antibacterial combinations of these amphiphiles were also identified. Amphiphiles in this study are composed of a benzene core with three benzylic ammonium bromide groups, two of which have alkyl chains, each 8-16 carbons in length. The third head group is a trimethylammonium or pyridinium. Log of critical aggregation concentration (log[CAC]) and heat of aggregation (ΔHagg) were both inversely proportional to the length of the linear hydrocarbon chains. Antibacterial activity increases with tail length until an optimal tail length of 12 carbons per chain, above which, activity decreased. The derivatives with two 12 carbon chains had the best antibacterial activity, killing all tested strains at concentrations of 1-2μM for Gram-positive and 4-16μM for Gram-negative bacteria. The identity of the third head group (trimethylammonium or pyridinium) had minimal effect on colloidal and antibacterial activity. The antibacterial activity of several binary combinations of amphiphiles from this study was higher than activity of individual amphiphiles, indicating that these combinations are synergistic. These amphiphiles show promise as novel antibacterial agents that could be used in a variety of applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Novel phytoceramides containing fatty acids of diverse chain lengths are better than a single C18-ceramide N-stearoyl phytosphingosine to improve the physiological properties of human stratum corneum

PubMed Central

Oh, Myoung Jin; Cho, Young Hoon; Cha, So Yoon; Lee, Eun Ok; Kim, Jin Wook; Kim, Sun Ki; Park, Chang Seo

2017-01-01

Ceramides in the human stratum corneum (SC) are a mixture of diverse N-acylated fatty acids (FAs) with different chain lengths. C24 is the major class of FAs of ceramides. However, there are also other classes of ceramides with diverse chain lengths of FAs, and these lengths generally range from C16 to C26. This study aimed to prepare several types of phytoceramide containing diverse chain lengths of N-acylated FAs and compare them with C18-ceramide N-stearoyl phytosphingosine (NP) in terms of their effects on the physiological properties of the SC. We chose natural oils, such as horse fat oil, shea butter, sunflower oil, and a mixture of macadamia nut, shea butter, moringa, and meadowfoam seed oil, as sources of FAs and phytosphingosine as a sphingoid backbone to synthesize diverse phytoceramides. Each phytoceramide exhibited a distinctive formation of the lamellar structure, and their FA profiles were similar to those of their respective natural oil. The skin barrier properties, as analyzed in human skin, clearly demonstrated that all the phytoceramides improved the recovery rate of the damaged SC and enhanced hydration better than C18-ceramide NP did. In conclusion, natural oil-derived phytoceramides could represent a novel class of ceramides for cosmetic applications in the development of an ideal skin barrier moisturizer. PMID:28979153

Alkyl chain interaction at the surface of room temperature ionic liquids: systematic variation of alkyl chain length (R = C(1)-C(4), C(8)) in both cation and anion of [RMIM][R-OSO(3)] by sum frequency generation and surface tension.

PubMed

Santos, Cherry S; Baldelli, Steven

2009-01-29

The gas-liquid interface of halide-free 1,3-dialkylimidazolium alkyl sulfates [RMIM][R-OSO(3)] with R chain length from C(1)-C(4) and C(8) has been studied systematically using the surface-specific sum frequency generation (SFG) vibrational spectroscopy and surface tension measurements. From the SFG spectra, vibrational modes from the methyl group of both cation and anion are observed for all ionic liquid samples considered in the present study. These results suggest the presence of both ions at the gas-liquid interface, which is further supported by surface tension measurements. Surface tension data show a decreasing trend as the alkyl chain in the imidazolium cation is varied from methyl to butyl chain, with a specific anion. A similar trend is observed when the alkyl chain of the anion is modified and the cation is fixed.

Peroxy radical detection by chemical amplification (PERCA)

NASA Technical Reports Server (NTRS)

Stedman, D. H.

1986-01-01

Important reactions of atmospheric free radicals are the chain oxidation of NO and CO. Thus: H2O + NO yields OH + NO2; OH + CO yields H + CO2; H + O2 + M yields HO2 + M. In most models, the need to know the free radical concentration could also be described as the need to know the rate of the above oxidation chain in the atmosphere. It is the total rate of this chain (also carried by RO2 and RO) which was measured using the PERCA. The PERCA is thus essentially a RO sub X meter. The PERCA works by adding excess CO (10%) and NO (5ppm) to a stream of air and measuring the NO2 produced after 3s of reaction time. Since other processes produce NO2, the chain reaction is modulated by switching the CO for N2. The chain length is limited by the reaction OH + NO yields HONO and is modeled to be somewhat over 1000. Measured chain lengths agree with the modeled numbers.

A potential bioactive hard-stock fat replacer comprised of a molecular gel.

PubMed

Rogers, Michael A; Spagnuolo, Paul A; Wang, Tzu-Min; Angka, Leonard

2017-05-01

Short-chain ceramides, such as N -acetoyl-d-erythro-sphingosine (C2), have a remarkable ability to structure edible oils, such as canola oil, into self-standing organogels without any added saturated or trans fats. These short-chain ceramides are ubiquitously found in foods ranging from eggs to soybeans. As the ceramide fatty acid chain length increases, there is an increase in the melting temperature of the organogel and a decrease in the elastic modulus. Gelation ability is lost at 2 wt% when the fatty acid chain length increases to six carbons; however, organogels form at 5 wt% up to 18 carbons. Short-chain ceramides, C2, decrease cell viability of colon, prostate, ovarian, and leukemia cell lines, while ceramides with long-chain fatty acids, C18, do not affect the viability of these cancer cell lines. This suggests that a bioactive spreadable fat, with no trans or added saturated fat, with the potential to alter the viability of cancer cell growth, is possible.

Interaction of cationic surfactants with DNA: a single-molecule study

PubMed Central

Husale, Sudhir; Grange, Wilfried; Karle, Marc; Bürgi, Stephan; Hegner, Martin

2008-01-01

The interaction of cationic surfactants with single dsDNA molecules has been studied using force-measuring optical tweezers. For hydrophobic chains of length 12 and greater, pulling experiments show characteristic features (e.g. hysteresis between the pulling and relaxation curves, force-plateau along the force curves), typical of a condensed phase (compaction of a long DNA into a micron-sized particle). Depending on the length of the hydrophobic chain of the surfactant, we observe different mechanical behaviours of the complex (DNA-surfactants), which provide evidence for different binding modes. Taken together, our measurements suggest that short-chain surfactants, which do not induce any condensation, could lie down on the DNA surface and directly interact with the DNA grooves through hydrophobic–hydrophobic interactions. In contrast, long-chain surfactants could have their aliphatic tails pointing away from the DNA surface, which could promote inter-molecular interactions between hydrophobic chains and subsequently favour DNA condensation. PMID:18203749

Can the scaling behavior of electric conductivity be used to probe the self-organizational changes in solution with respect to the ionic liquid structure? The case of [C8MIM][NTf2].

PubMed

Paluch, Marian; Wojnarowska, Zaneta; Goodrich, Peter; Jacquemin, Johan; Pionteck, Jürgen; Hensel-Bielowka, Stella

2015-08-28

Electrical conductivity of the supercooled ionic liquid [C8MIM][NTf2], determined as a function of temperature and pressure, highlights strong differences in its ionic transport behavior between low and high temperature regions. To date, the crossover effect which is very well known for low molecular van der Waals liquids has been rarely described for classical ionic liquids. This finding highlights that the thermal fluctuations could be dominant mechanisms driving the dramatic slowing down of ion motions near Tg. An alternative way to analyze separately low and high temperature dc-conductivity data using a density scaling approach was then proposed. Based on which a common value of the scaling exponent γ = 2.4 was obtained, indicating that the applied density scaling is insensitive to the crossover effect. By comparing the scaling exponent γ reported herein along with literature data for other ionic liquids, it appears that γ decreases by increasing the alkyl chain length on the 1-alkyl-3-methylimidazolium-based ionic liquids. This observation may be related to changes in the interaction between ions in solution driven by an increase in the van der Waals type interaction by increasing the alkyl chain length on the cation. This effect may be related to changes in the ionic liquid nanostructural organization with the alkyl chain length on the cation as previously reported in the literature based on molecular dynamic simulations. In other words, the calculated scaling exponent γ may be then used as a key parameter to probe the interaction and/or self-organizational changes in solution with respect to the ionic liquid structure.

Effect of surfactant chain length on drug release kinetics from microemulsion-laden contact lenses.

PubMed

Maulvi, Furqan A; Desai, Ankita R; Choksi, Harsh H; Patil, Rahul J; Ranch, Ketan M; Vyas, Bhavin A; Shah, Dinesh O

2017-05-30

The effect of surfactant chain lengths [sodium caprylate (C 8 ), Tween 20 (C 12 ), Tween 80 (C 18 )] and the molecular weight of block copolymers [Pluronic F68 and Pluronic F 127] were studied to determine the stability of the microemulsion and its effect on release kinetics from cyclosporine-loaded microemulsion-laden hydrogel contact lenses in this work. Globule size and dilution tests (transmittance) suggested that the stability of the microemulsion increases with increase in the carbon chain lengths of surfactants and the molecular weight of pluronics. The optical transmittance of direct drug-laden contact lenses [DL-100] was low due to the precipitation of hydrophobic drugs in the lenses, while in microemulsion-laden lenses, the transmittance was improved when stability of the microemulsion was achieved. The results of in vitro release kinetics revealed that drug release was sustained to a greater extent as the stability of microemulsion was improved as well. This was evident in batch PF127-T80, which showed sustained release for 15days in comparison to batch DL-100, which showed release up to 7days. An in vivo drug release study in rabbit tear fluid showed significant increase in mean residence time (MRT) and area under curve (AUC) with PF-127-T80 lenses (stable microemulsion) in comparison to PF-68-SC lenses (unstable microemulsion) and DL-100 lenses. This study revealed the correlation between the stability of microemulsion and the release kinetics of drugs from contact lenses. Thus, it was inferred that the stable microemulsion batches sustained the release of hydrophobic drugs, such as cyclosporine from contact lenses for an extended period of time without altering critical lens properties. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

Structure-activity relationships of 4-hydroxyalkenals in the conjugation catalysed by mammalian glutathione transferases.

PubMed Central

Danielson, U H; Esterbauer, H; Mannervik, B

1987-01-01

The substrate specificities of 15 cytosolic glutathione transferases from rat, mouse and man have been explored by use of a homologous series of 4-hydroxyalkenals, extending from 4-hydroxypentenal to 4-hydroxypentadecenal. Rat glutathione transferase 8-8 is exceptionally active with the whole range of 4-hydroxyalkenals, from C5 to C15. Rat transferase 1-1, although more than 10-fold less efficient than transferase 8-8, is the second most active transferase with the longest chain length substrates. Other enzyme forms showing high activities with these substrates are rat transferase 4-4 and human transferase mu. The specificity constants, kcat./Km, for the various enzymes have been determined with the 4-hydroxyalkenals. From these constants the incremental Gibbs free energy of binding to the enzyme has been calculated for the homologous substrates. The enzymes responded differently to changes in the length of the hydrocarbon side chain and could be divided into three groups. All glutathione transferases displayed increased binding energy in response to increased hydrophobicity of the substrate. For some of the enzymes, steric limitations of the active site appear to counteract the increase in binding strength afforded by increased chain length of the substrate. Comparison of the activities with 4-hydroxyalkenals and other activated alkenes provides information about the active-site properties of certain glutathione transferases. The results show that the ensemble of glutathione transferases in a given species may serve an important physiological role in the conjugation of the whole range of 4-hydroxyalkenals. In view of its high catalytic efficiency with all the homologues, rat glutathione transferase 8-8 appears to have evolved specifically to serve in the detoxication of these reactive compounds of oxidative metabolism. PMID:3426557

High data density and capacity in chipless radiofrequency identification (chipless-RFID) tags based on double-chains of S-shaped split ring resonators (S-SRRs)

NASA Astrophysics Data System (ADS)

Herrojo, Cristian; Mata-Contreras, Javier; Paredes, Ferran; Martín, Ferran

2017-11-01

The data density per surface (DPS) is a figure of merit in chipless radiofrequency identification (chipless-RFID) tags. In this paper, it is demonstrated that chipless-RFID tags with high DPS can be implemented by using double-chains of S-shaped split ring resonators (S-SRRs). Tag reading is achieved by near-field coupling between the tag and the reader, a CPW transmission line fed by a harmonic signal tuned to the resonance frequency of the S-SRRs. By transversally displacing the tag over the CPW, the transmission coefficient of the line is modulated by tag motion. This effectively modulates the amplitude of the injected (carrier) signal at the output port of the line, and the identification (ID) code, determined by the presence or absence of S-SRRs at predefined and equidistant positions in the chains, is contained in the envelope function. The DPS is determined by S-SRR dimensions and by the distance between S-SRRs in the chains. However, by using two chains of S-SRRs, the number of bits per unit length that can be accommodated is very high. This chipless-RFID system is of special interest in applications where the reading distance can be sacrificed in favor of data capacity (e.g., security and authentication). Encoding of corporate documents, ballots, exams, etc., by directly printing the proposed tags on the item product to prevent counterfeiting is envisaged.

Inhibition of dog and human gastric lipases by enantiomeric phosphonate inhibitors: a structure-activity study.

PubMed

Miled, Nabil; Roussel, Alain; Bussetta, Cécile; Berti-Dupuis, Liliane; Rivière, Mireille; Buono, Gérard; Verger, Robert; Cambillau, Christian; Canaan, Stéphane

2003-10-14

The crystal structures of gastric lipases in the apo form [Roussel, A., et al. (1999) J. Biol. Chem. 274, 16995-17002] or in complex with the (R(P))-undecyl butyl phosphonate [C(11)Y(4)(+)] [Roussel, A., et al. (2002) J. Biol. Chem. 277, 2266-2274] have improved our understanding of the structure-activity relationships of acid lipases. In this report, we have performed a kinetic study with dog and human gastric lipases (DGL and HGL, respectively) using several phosphonate inhibitors by varying the absolute configuration of the phosphorus atom and the chain length of the alkyl/alkoxy substituents. Using the two previously determined structures and that of a new crystal structure obtained with the other (S(P))-phosphonate enantiomer [C(11)Y(4)(-)], we constructed models of phosphonate inhibitors fitting into the active site crevices of DGL and HGL. All inhibitors with a chain length of fewer than 12 carbon atoms were found to be completely buried in the catalytic crevice, whereas longer alkyl/alkoxy chains were found to point out of the cavity. The main stereospecific determinant explaining the stronger inhibition of the S(P) enantiomers is the presence of a hydrogen bond involving the catalytic histidine as found in the DGL-C(11)Y(4)(-) complex. On the basis of these results, we have built a model of the first tetrahedral intermediate corresponding to the tristearoyl-lipase complex. The triglyceride molecule completely fills the active site crevice of DGL, in contrast with what is observed with other lipases such as pancreatic lipases which have a shallower and narrower active site. For substrate hydrolysis, the supply of water molecules to the active site might be achieved through a lateral channel identified in the protein core.

Folding dynamics of linear emulsion polymers into 3D architectures

NASA Astrophysics Data System (ADS)

McMullen, Angus; Bargteil, Dylan; Brujic, Jasna

Colloidal polymers have been limited to inflexible, solid colloids. Here we show that the fluidity of emulsion droplets allows for the self-assembly of flexible droplet chains, which can subsequently be folded into 3D structures via secondary interactions. We achieve this using DNA-guided interactions, to initially form the chain, and then program its folding pathways. When two emulsion droplets labeled with complementary DNA meet, the balance of hybridization energy and droplet deformation yields an equilibrium patch size. Therefore, the concentration of DNA on the surface determines the number of droplet-droplet bonds in the assembly. We find that 96 % of bound droplets successfully self-assemble into chains. Droplet binding is a stochastic process, following a Poisson distribution of lengths. Since the fluid droplets can rearrange, we compare the dynamics of emulsion chains to that of polymers. We also trigger secondary interactions along the chain, causing the formation of specific loops or compact clusters. This approach will allow us to fold our emulsion polymers into a wide array of soft structures, giving us a powerful biomimetic colloidal system to investigate protein folding on the mesoscopic scale. This work was supported by the NSF MRSEC Program (DMR-0820341).

Tension amplification in tethered layers of bottle-brush polymers

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

Leuty, Gary M.; Tsige, Mesfin; Grest, Gary S.

2016-02-26

In this paper, molecular dynamics simulations of a coarse-grained bead–spring model have been used to study the effects of molecular crowding on the accumulation of tension in the backbone of bottle-brush polymers tethered to a flat substrate. The number of bottle-brushes per unit surface area, Σ, as well as the lengths of the bottle-brush backbones N bb (50 ≤ N bb ≤ 200) and side chains N sc (50 ≤ N sc ≤ 200) were varied to determine how the dimensions and degree of crowding of bottle-brushes give rise to bond tension amplification along the backbone, especially near the substrate.more » From these simulations, we have identified three separate regimes of tension. For low Σ, the tension is due solely to intramolecular interactions and is dominated by the side chain repulsion that governs the lateral brush dimensions. With increasing Σ, the interactions between bottle-brush polymers induce compression of the side chains, transmitting increasing tension to the backbone. For large Σ, intermolecular side chain repulsion increases, forcing side chain extension and reorientation in the direction normal to the surface and transmitting considerable tension to the backbone.« less

Thermal aging of interfacial polymer chains in ethylene-propylene-diene terpolymer/aluminum hydroxide composites: solid-state NMR study.

PubMed

Gabrielle, Brice; Lorthioir, Cédric; Lauprêtre, Françoise

2011-11-03

The possible influence of micrometric-size filler particles on the thermo-oxidative degradation behavior of the polymer chains at polymer/filler interfaces is still an open question. In this study, a cross-linked ethylene-propylene-diene (EPDM) terpolymer filled by aluminum trihydrate (ATH) particles is investigated using (1)H solid-state NMR. The time evolution of the EPDM network microstructure under thermal aging at 80 °C is monitored as a function of the exposure time and compared to that of an unfilled EPDM network displaying a similar initial structure. While nearly no variations of the topology are observed on the neat EPDM network over 5 days at 80 °C, a significant amount of chain scission phenomena are evidenced in EPDM/ATH. A specific surface effect induced by ATH on the thermodegradative properties of the polymer chains located in their vicinity is thus pointed out. Close to the filler particles, a higher amount of chain scissions are detected, and the characteristic length scale related to these interfacial regions displaying a significant thermo-oxidation process is determined as a function of the aging time.

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

PubMed

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

2006-08-17

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

Cuticular hydrocarbons as a tool for the identification of insect species: Puparial cases from Sarcophagidae

PubMed Central

Braga, Marina Vianna; Pinto, Zeneida Teixeira; de Carvalho Queiroz, Margareth Maria; Matsumoto, Nana; Blomquist, Gary James

2013-01-01

The external surface of all insects is covered by a species-specific complex mixture of highly stable, very long chain cuticular hydrocarbons (CHCs). Gas chromatography coupled to mass spectrometry was used to identify CHCs from four species of Sarcophagidae, Peckia (Peckia) chrysostoma, Peckia (Pattonella) intermutans, Sarcophaga (Liopygia) ruficornis and Sarcodexia lambens. The identified CHCs were mostly a mixture of n-alkanes, monomethylalkanes and dimethylalkanes with linear chain lengths varying from 23 to 33 carbons. Only two alkenes were found in all four species. S. lambens had a composition of CHCs with linear chain lengths varying from C23 to C33, while the other three species linear chain lengths from 24 to 31 carbons. n-Heptacosane, n-nonacosane and 3-methylnonacosane, n-triacontane and n-hentriacontane occurred in all four species. The results show that these hydrocarbon profiles may be used for the taxonomic differentiation of insect species and are a useful additional tool for taxonomic classification, especially when only parts of the insect specimen are available. PMID:23932943

Mutant fatty acid desaturase

DOEpatents

Shanklin, John; Cahoon, Edgar B.

2004-02-03

The present invention relates to a method for producing mutants of a fatty acid desaturase having a substantially increased activity towards fatty acid substrates with chains containing fewer than 18 carbons relative to an unmutagenized precursor desaturase having an 18 carbon atom chain length substrate specificity. The method involves inducing one or more mutations in the nucleic acid sequence encoding the precursor desaturase, transforming the mutated sequence into an unsaturated fatty acid auxotroph cell such as MH13 E. coli, culturing the cells in the absence of supplemental unsaturated fatty acids, thereby selecting for recipient cells which have received and which express a mutant fatty acid desaturase with an elevated specificity for fatty acid substrates having chain lengths of less than 18 carbon atoms. A variety of mutants having 16 or fewer carbon atom chain length substrate specificities are produced by this method. Mutant desaturases produced by this method can be introduced via expression vectors into prokaryotic and eukaryotic cells and can also be used in the production of transgenic plants which may be used to produce specific fatty acid products.

Computational Design of High-χ Block Oligomers for Accessing 1 nm Domains.

PubMed

Chen, Qile P; Barreda, Leonel; Oquendo, Luis E; Hillmyer, Marc A; Lodge, Timothy P; Siepmann, J Ilja

2018-05-22

Molecular dynamics simulations are used to design a series of high-χ block oligomers (HCBOs) that can self-assemble into a variety of mesophases with domain sizes as small as 1 nm. The exploration of these oligomers with various chain lengths, volume fractions, and chain architectures at multiple temperatures reveals the presence of ordered lamellae, perforated lamellae, and hexagonally packed cylinders. The achieved periods are as small as 3.0 and 2.1 nm for lamellae and cylinders, respectively, which correspond to polar domains of approximately 1 nm. Interestingly, the detailed phase behavior of these oligomers is distinct from that of either solvent-free surfactants or block polymers. The simulations reveal that the behavior of these HCBOs is a product of an interplay between both "surfactant factors" (headgroup interactions, chain flexibility, and interfacial curvature) and "block polymer factors" (χ, chain length N, and volume fraction f). This insight promotes the understanding of molecular features pivotal for mesophase formation at the sub-5 nm length scale, which facilitates the design of HCBOs tailored toward particular desired morphologies.

Length-scale and strain rate-dependent mechanism of defect formation and fracture in carbon nanotubes under tensile loading

NASA Astrophysics Data System (ADS)

Javvaji, Brahmanandam; Raha, S.; Mahapatra, D. Roy

2017-02-01

Electromagnetic and thermo-mechanical forces play a major role in nanotube-based materials and devices. Under high-energy electron transport or high current densities, carbon nanotubes fail via sequential fracture. The failure sequence is governed by certain length scale and flow of current. We report a unified phenomenological model derived from molecular dynamic simulation data, which successfully captures the important physics of the complex failure process. Length-scale and strain rate-dependent defect nucleation, growth, and fracture in single-walled carbon nanotubes with diameters in the range of 0.47 to 2.03 nm and length which is about 6.17 to 26.45 nm are simulated. Nanotubes with long length and small diameter show brittle fracture, while those with short length and large diameter show transition from ductile to brittle fracture. In short nanotubes with small diameters, we observe several structural transitions like Stone-Wales defect initiation, its propagation to larger void nucleation, formation of multiple chains of atoms, conversion to monatomic chain of atoms, and finally complete fracture of the carbon nanotube. Hybridization state of carbon-carbon bonds near the end cap evolves, leading to the formation of monatomic chain in short nanotubes with small diameter. Transition from ductile to brittle fracture is also observed when strain rate exceeds a critical value. A generalized analytical model of failure is established, which correlates the defect energy during the formation of atomic chain with aspect ratio of the nanotube and strain rate. Variation in the mechanical properties such as elastic modulus, tensile strength, and fracture strain with the size and strain rate shows important implications in mitigating force fields and ways to enhance the life of electronic devices and nanomaterial conversion via fracture in manufacturing.

Some effects of long chain polymethylene bisonium salts on junctional transmission in the peripheral nervous system

PubMed Central

Barlow, R. B.; Zoller, Anne

1964-01-01

A survey has been made of the effects on junctional transmission of the complete series of polymethylene bis-trimethylammonium (BTM) and bis-triethylammonium (BTE) salts from the decamethylene compounds (BTM 10 and BTE 10) to those with twenty-one methylene groups in the chain. These were tested for their ability to cause contracture of the isolated chick biventer cervicis preparation, and for their ability to block the twitch responses of this preparation, those of the rat isolated diaphragm preparation, and those of the cat tibialis anterior preparation. They were also tested for their ability to block transmission in the cat superior cervical ganglion, to block the actions of acetylcholine on the guinea-pig isolated ileum, and for ability to inhibit the hydrolysis of acetylcholine by acetylcholinesterase. Their electrical conductivity has been measured in aqueous solution. Ability to cause contracture of the chick biventer cervicis is confined to the compounds BTM 10 to 15; BTE 10, 11 and 12 have some weak activity but the other BTE compounds, and the BTM compounds with more than fifteen methylene groups, have virtually no activity. In the BTE series both neuromuscular blocking and ganglion-blocking activities increase with chain length up to a maximum in the region of BTE 15 to 17 and then decline. In the BTM series ganglion-blocking activity increases with chain length in much the same way as in the BTE series, though the maximum activity is at a slightly longer chain length. At the neuromuscular junction an increase in chain length beyond BTM 10 leads to a decline in activity but this returns to some extent at longer chain lengths, reaching a second maximum at BTM 18, above which it declines further. At the ganglion BTE 16 is only slightly more active than BTM 16 and about five-times as active as hexamethonium; at the neuromuscular junction in the cat BTE 16 is about five-times as active as BTM 16 and about eight-times as active as (+)-tubocurarine. The affinity of the BTE compounds for the postganglionic acetylcholine receptors of the guinea-pig ileum reaches a maximum at BTE 14 but does not decline significantly with further increase in chain length. Anticholinesterase activity, likewise, does not alter significantly between BTM 12 and BTM 21 and the activity of the compounds in the BTE series appears to be similar. This property could conceivably be modifying the actions of some of the intermediate compounds but is not likely to be affecting those of the more active ones. The conductivity experiments indicate that micelle formation could be limiting the actions of the compounds with 20 or 21 methylene groups, but is not likely to be affecting those of the other compounds. The results suggest that there is a regular increase with chain length of the affinity of these compounds for the receptors in the ganglia and at the neuromuscular junction but that efficacy in causing contracture is limited to compounds with three methyl groups in the cationic head and a chain of about ten methylene groups. The connexion between this ability to depolarize and the ability to block transmission by desensitization is discussed. PMID:14208190

Self-Assembled Monolayers of Dithiophosphinic Acids on Gold

NASA Astrophysics Data System (ADS)

San Juan, Ronan Roca

This dissertation reports the synthesis of derivatives of dithiophosphinic acids (R1R2DTPAs), and the formation and characterization of DTPA SAMs on gold to build a knowledge base on their nature of binding, organization of the alkyl chains and electrochemical barrier properties. The binding of DTPA molecules on gold depends on the morphology of the gold film: They bind in a mixed monodentate and bidentate modes on standard as-deposited (As-Dep) gold, while they fully chelate on smoother template-stripped (TS) gold. Chapter 2 focuses on van der Waals interactions of various alkyl chain lengths of symmetrical R2DTPA SAMs, which increase with increasing chain lengths similar to those of the analogous n-alkanethiol SAMs, but with alkyl chains that are generally less dense than those of n-alkanethiol SAMs. Chapter 3 addresses why the DTPA compounds do not chelate on the standard As-Dep gold by comparing (C16)2DTPA SAM to (C16 )2DDP SAM. Here, side chain crystallinity stabilizes DTPA SAM structure at the expense of chelation of the DTPA molecules, which leads to a mixture of bidentate and monodentate DTPA molecules, whereas the increased flexibility of the chains in DDP due to the oxygen atoms retains chelation of the DDP molecules. Chapter 4 focuses on the SAMs formed from RlongRshort DTPAs, which shows that the length of the short chain spacer affects SAM packing density and thickness. The SAMs of these molecules also show homogeneous mixing of Rlong and Rshort chains. Chapter 5 investigates PhRDTPA SAMs in preparation for molecular junction studies. The chelation of PhRDTPA molecules on TS gold allows the PhRDTPAs to act as molecular alligator clips. The length of the alkyl chains controls the density of the phenyl group and they fill in the voids between adsorbates to prevent electrical shorting. Finally, Chapter 6 incorporates OH tail group(s) to control the wettability of DTPA SAMs. The presence of OH groups in DTPAs forms hydrophilic SAMs. The symmetrical OH-terminated DTPA forms a SAM with similar packing density to that of an analogous CH3-terminated DTPA SAM, while the OH/CH 3-terminated DTPA forms a thin SAM with low molecular packing, however, the chains of this SAM are homogeneously mixed.

Development of environmentally friendly coatings and paints using medium-chain-length poly(3-hydroxyalkanoates) as the polymer binder.

PubMed

van der Walle, G A; Buisman, G J; Weusthuis, R A; Eggink, G

1999-01-01

Unsaturated medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs) produced by Pseudomonas putida from linseed oil fatty acids (LOFA) and tall oil fatty acids (TOFA), were used as the polymer binder in the formulation of high solid alkyd-like paints. The relatively high concentration of unsaturated alkyl side chains incorporated into the PHA resins resulted in oxidative drying PHA paints having excellent coating properties. The homogeneously pigmented PHA coatings yielded high-gloss, smooth and strong films upon curing and showed an excellent flexibility, a good adhesion to different substrates, cohesive film properties and resistance to chipping.

Small Subunits of Serine Palmitoyltransferase (ssSPTs) and Their Physiological Roles

DTIC Science & Technology

2014-02-12

showing that organisms also have unique sphingoid base chain lengths. In insects, such as Drosophila melanogaster , the predominant chain lengths of the ... Drosophila melanogaster mutant defective in male meiotic cytokinesis (‘Ghiberti’) has a mutation in a gene with low homology to the ssSPT subunits of...INTRODUCTION: Sphingolipid metabolism in Drosophila melanogaster (fly) is an active area of research. It is a good model system to study the roles of

The scent of mixtures: rules of odour processing in ants

PubMed Central

Perez, Margot; Giurfa, Martin; d'Ettorre, Patrizia

2015-01-01

Natural odours are complex blends of numerous components. Understanding how animals perceive odour mixtures is central to multiple disciplines. Here we focused on carpenter ants, which rely on odours in various behavioural contexts. We studied overshadowing, a phenomenon that occurs when animals having learnt a binary mixture respond less to one component than to the other, and less than when this component was learnt alone. Ants were trained individually with alcohols and aldehydes varying in carbon-chain length, either as single odours or binary mixtures. They were then tested with the mixture and the components. Overshadowing resulted from the interaction between chain length and functional group: alcohols overshadowed aldehydes, and longer chain lengths overshadowed shorter ones; yet, combinations of these factors could cancel each other and suppress overshadowing. Our results show how ants treat binary olfactory mixtures and set the basis for predictive analyses of odour perception in insects. PMID:25726692

Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates

DOE PAGES

Xia, Yan; Li, Ming; Charubin, Kamil; ...

2015-11-05

In this paper, we report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C 14, DMPC) in discoidal “bicelles” (0.156 h –1) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10 –3 h –1). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C 14 DMPC to di-C 16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differentialmore » scanning calorimetry (DSC), and fluorescence correlation spectroscopy (FCS) are in good agreement. Finally, the present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.« less

Kinetic aspects of the coil-stretch transition of polymer chains in dilute solution under extensional flow

NASA Astrophysics Data System (ADS)

Hernández Cifre, J. G.; García de la Torre, J.

2001-11-01

When linear polymer chains in dilute solution are subject to extensional flow, each chain in the sample experiences the coil-stretch transition at a different time. Using Brownian dynamics simulation, we have studied the distribution of transition times in terms of the extensional rate and the length of the chains. If instead of time one characterizes the effect of the flow by the accumulated strain, then the distribution and its moments seem to take general forms, independent of molecular weight and flow rate, containing some numerical, universal constants that have been evaluated from the dynamical simulation. The kinetics of the transition, expressed by the time-dependence of the fraction of remaining coils, has also been simulated, and the results for the kinetic rate constant has been rationalized in a manner similar to that used for the transition time. The molecular individualism, characterized in this work by the distribution of transition times, is related to the excess of the applied extensional rate over its critical value, which will determine the transition time and other features of the coil-stretch transition.

Subsampled Numerical Experiments as a Guide for Field Deployment of Thermistor Chains

NASA Astrophysics Data System (ADS)

Shaw, Justin; Stastna, Marek

2017-11-01

Thermistor chains are a standard tool for recording temperature profiles in geophysical flows. Density values can be inferred from readings and the resulting density field analyzed for the passage of internal waves, Kelvin-Helmholtz billows, and other dynamic events. The number and spacing of the thermistors, both on and between chains, determines which events can be identified in the dataset. We examine the effect of changing these variables by subsampling a set of numerical experiments to simulate thermistor chain locations. A pseudo spectral method was used to solve the incompressible Navier-Stokes equations under the Boussinesq approximation. The resulting flows are a set of high resolution seiches where the depth was held constant across experiments, and the length was varied. Sampling a known, commonly occurring flow with relatively simple geometry allows for a clear analysis of the effects of thermistor placement in the capture of dynamic events. We will discuss three dimensional deployment strategies, as well as EOF and DMD analyses if there is time. Funded by a Grant from the National Sciences and Engineering Research Council of Canada.

Effect of DEXTRAN-graft-POLYACRYLAMIDE Internal Structure on Flocculation Process Parameters

NASA Astrophysics Data System (ADS)

Bezugla, T.; Kutsevol, N.; Shyichuk, A.; Ziolkowska, D.

2008-08-01

Dextran-graft-Polyacrylamide copolymers (D-g-PAA) of brush-like architecture were tested as flocculation aids in the model kaolin suspensions. Due to expanded conformation the D-g-PAA copolymers are more effective flocculants than individual PAA with close molecular mass. The internal structure of D-g-PAA copolymers which is determined by number and length of grafted PAA chains, the distance between grafts, etc., has the significant influence on flocculation behavior of such polymers.

Finding the Missing Physics: Simulating Polydisperse Polymer Melts

NASA Astrophysics Data System (ADS)

Rorrer, Nichoals; Dorgan, John

2014-03-01

A Monte Carlo algorithm has been developed to model polydisperse polymer melts. For the first time, this enables the specification of a predetermined molecular weight distribution for lattice based simulations. It is demonstrated how to map an arbitrary probability distributions onto a discrete number of chains residing on an fcc lattice. The resulting algorithm is able to simulate a wide variety of behaviors for polydisperse systems including confinement effects, shear flow, and parabolic flow. The dynamic version of the algorithm accurately captures Rouse dynamics for short polymer chains, and reptation-like dynamics for longer chain lengths.1 When polydispersity is introduced, smaller Rouse times and broadened the transition between different scaling regimes are observed. Rouse times also decrease under confinement for both polydisperse and monodisperse systems and chain length dependent migration effects are observed. The steady-state version of the algorithm enables the simulation of flow and when polydisperse systems are subject to parabolic (Poiseulle) flow, a migration phenomenon based on chain length is again present. These and other phenomena highlight the importance of including polydispersity in obtaining physically realistic simulations of polymeric melts. 1. Dorgan, J.R.; Rorrer, N.A.; Maupin, C.M., Macromolecules 2012, 45(21), 8833-8840. Work funded by the Fluid Dynamics program of the National Science Foundation under grant CBET-1067707.

The effects of chain length, embedded polar groups, pressure, and pore shape on structure and retention in reversed-phase liquid chromatography: molecular-level insights from Monte Carlo simulations.

PubMed

Rafferty, Jake L; Siepmann, J Ilja; Schure, Mark R

2009-03-20

Particle-based simulations using the configurational-bias and Gibbs ensemble Monte Carlo techniques are carried out to probe the effects of various chromatographic parameters on bonded-phase chain conformation, solvent penetration, and retention in reversed-phase liquid chromatography (RPLC). Specifically, we investigate the effects due to the length of the bonded-phase chains (C(18), C(8), and C(1)), the inclusion of embedded polar groups (amide and ether) near the base of the bonded-phase chains, the column pressure (1, 400, and 1000 atm), and the pore shape (planar slit pore versus cylindrical pore with a 60A diameter). These simulations utilize a bonded-phase coverage of 2.9 micromol/m(2)and a mobile phase containing methanol at a molfraction of 33% (about 50% by volume). The simulations show that chain length, embedded polar groups, and pore shape significantly alter structural and retentive properties of the model RPLC system, whereas the column pressure has a relatively small effect. The simulation results are extensively compared to retention measurements. A molecular view of the RPLC retention mechanism emerges that is more complex than can be inferred from thermodynamic measurements.

Softening of the stiffness of bottle-brush polymers by mutual interaction

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

Bolisetty, S.; Airaud, C.; Rosenfeldt, S.

2007-04-15

We study bottle-brush macromolecules in a good solvent by small-angle neutron scattering (SANS), static light scattering (SLS), and dynamic light scattering (DLS). These polymers consist of a linear backbone to which long side chains are chemically grafted. The backbone contains about 1600 monomer units (weight average) and every second monomer unit carries side chains with approximately 60 monomer units. The SLS and SANS data extrapolated to infinite dilution lead to the form factor of the polymer that can be described in terms of a wormlike chain with a contour length of 380 nm and a persistence length of 17.5 nm.more » An analysis of the DLS data confirms these model parameters. The scattering intensities taken at finite concentration can be modeled using the polymer reference interaction site model. It reveals a softening of the bottle-brush polymers caused by their mutual interaction. We demonstrate that the persistence decreases from 17.5 nm down to 5 nm upon increasing the concentration from dilute solution to the highest concentration (40.59 g/l) under consideration. The observed softening of the chains is comparable to the theoretically predicted decrease of the electrostatic persistence length of linear polyelectrolyte chains at finite concentrations.« less

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

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

Putra, Edy Giri Rachman; Patriati, Arum; Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Gadjah Mada, Bulaksumur, Yogyakarta 55281, Indonesia giri@batan.go.id

2015-04-16

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2–10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30–50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol,more » octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.« less

Influence of the molecular architecture on the adsorption onto solid surfaces: comb-like polymers.

PubMed

Guzmán, Eduardo; Ortega, Francisco; Prolongo, Margarita G; Starov, Victor M; Rubio, Ramón G

2011-09-28

The processes of adsorption of grafted copolymers onto negatively charged surfaces were studied using a dissipative quartz crystal microbalance (D-QCM) and ellipsometry. The control parameters in the study of the adsorption are the existence or absence on the molecular architecture of grafted polyethyleneglycol (PEG) chains with different lengths and the chemical nature of the main chain, poly(allylamine) (PAH) or poly(L-lysine) (PLL). It was found out that the adsorption kinetics of the polymers showed a complex behavior. The total adsorbed amount depends on the architecture of the polymer chains (length of the PEG chains), on the polymer concentration and on the chemical nature of the main chain. The comparison of the thicknesses of the adsorbed layers obtained from D-QCM and from ellipsometry allowed calculation of the water content of the layers that is intimately related to the grafting length. The analysis of D-QCM results also provides information about the shear modulus of the layers, whose values have been found to be typical of a rubber-like polymer system. It is shown that the adsorption of polymers with a charged backbone is not driven exclusively by the electrostatic interactions, but the entropic contributions as a result of the trapping of water in the layer structure are of fundamental importance.

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

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

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Using Games to Teach Markov Chains

ERIC Educational Resources Information Center

Johnson, Roger W.

2003-01-01

Games are promoted as examples for classroom discussion of stationary Markov chains. In a game context Markov chain terminology and results are made concrete, interesting, and entertaining. Game length for several-player games such as "Hi Ho! Cherry-O" and "Chutes and Ladders" is investigated and new, simple formulas are given. Slight…

Modulatory effects of heparin and short-length oligosaccharides of heparin on the metastasis and growth of LMD MDA-MB 231 breast cancer cells in vivo

PubMed Central

Mellor, P; Harvey, J R; Murphy, K J; Pye, D; O'Boyle, G; Lennard, T W J; Kirby, J A; Ali, S

2007-01-01

Expression of the chemokine receptor CXCR4 allows breast cancer cells to migrate towards specific metastatic target sites which constitutively express CXCL12. In this study, we determined whether this interaction could be disrupted using short-chain length heparin oligosaccharides. Radioligand competition binding assays were performed using a range of heparin oligosaccharides to compete with polymeric heparin or heparan sulphate binding to I125 CXCL12. Heparin dodecasaccharides were found to be the minimal chain length required to efficiently bind CXCL12 (71% inhibition; P<0.001). These oligosaccharides also significantly inhibited CXCL12-induced migration of CXCR4-expressing LMD MDA-MB 231 breast cancer cells. In addition, heparin dodecasaccharides were found to have less anticoagulant activity than either a smaller quantity of polymeric heparin or a similar amount of the low molecular weight heparin pharmaceutical product, Tinzaparin. When given subcutaneously in a SCID mouse model of human breast cancer, heparin dodecasaccharides had no effect on the number of lung metastases, but did however inhibit (P<0.05) tumour growth (lesion area) compared to control groups. In contrast, polymeric heparin significantly inhibited both the number (P<0.001) and area of metastases, suggesting a differing mechanism for the action of polymeric and heparin-derived oligosaccharides in the inhibition of tumour growth and metastases. PMID:17726466

Identification of verotoxin type 2 variant B subunit genes in Escherichia coli by the polymerase chain reaction and restriction fragment length polymorphism analysis.

PubMed Central

Tyler, S D; Johnson, W M; Lior, H; Wang, G; Rozee, K R

1991-01-01

A set of synthetic oligonucleotide primers was designed for use in a polymerase chain reaction protocol to specifically detect the B subunit genes in vtx2ha and vtx2hb, which code for the production of the VT2 (Shiga-like toxin II) variant cytotoxins VT2v-a and VT2v-b, respectively. An additional set of primers amplified a fragment common to the B subunits of the VT2 and the VT2 variant genes. Subsequent restriction endonuclease digestion of this amplicon permitted prediction of specific VT2 and variant genotypes on the basis of predetermined restriction fragment length polymorphisms. Genotypes of 21 VT2-producing strains of Escherichia coli were determined using this polymerase chain reaction-restriction fragment length polymorphism procedure. Four strains contained B subunit target sequences only for VT2 genes, 9 strains contained sequences only for VT2v-a genes, and 3 strains contained sequences only for VT2v-b. For genes in combination, one strain contained B subunit genes for both VT2 and VT2v-a and two strains contained B subunit genes for VT2 and VT2v-b. Two strains of E. coli O91:H21 contained both VT2v-a and VT2v-b B subunit genes. The VT2 reference strain of E. coli, E32511, was found to contain the targeted sequences from both VT2 and VT2v-a genes, whereas the recombinant E. coli, pEB1, possessed only that of the VT2 gene. The specific activities of extracellular VT2 determined in HeLa cells ranged from 0.3 to 41.7 TCD50 per microgram of protein in strains carrying the VT2 gene target and from 0 to 50.0 TCD50 per microgram of protein in strains carrying only the VT2 variant target (TCD50 is the tissue culture dose by which 50% of the cells were affected), suggesting that phenotypic expression does not correlate with genotype. Images PMID:1679436

An efficient and scalable extraction and quantification method for algal derived biofuel.

PubMed

Lohman, Egan J; Gardner, Robert D; Halverson, Luke; Macur, Richard E; Peyton, Brent M; Gerlach, Robin

2013-09-01

Microalgae are capable of synthesizing a multitude of compounds including biofuel precursors and other high value products such as omega-3-fatty acids. However, accurate analysis of the specific compounds produced by microalgae is important since slight variations in saturation and carbon chain length can affect the quality, and thus the value, of the end product. We present a method that allows for fast and reliable extraction of lipids and similar compounds from a range of algae, followed by their characterization using gas chromatographic analysis with a focus on biodiesel-relevant compounds. This method determines which range of biologically synthesized compounds is likely responsible for each fatty acid methyl ester (FAME) produced; information that is fundamental for identifying preferred microalgae candidates as a biodiesel source. Traditional methods of analyzing these precursor molecules are time intensive and prone to high degrees of variation between species and experimental conditions. Here we detail a new method which uses microwave energy as a reliable, single-step cell disruption technique to extract lipids from live cultures of microalgae. After extractable lipid characterization (including lipid type (free fatty acids, mono-, di- or tri-acylglycerides) and carbon chain length determination) by GC-FID, the same lipid extracts are transesterified into FAMEs and directly compared to total biodiesel potential by GC-MS. This approach provides insight into the fraction of total FAMEs derived from extractable lipids compared to FAMEs derived from the residual fraction (i.e. membrane bound phospholipids, sterols, etc.). This approach can also indicate which extractable lipid compound, based on chain length and relative abundance, is responsible for each FAME. This method was tested on three species of microalgae; the marine diatom Phaeodactylum tricornutum, the model Chlorophyte Chlamydomonas reinhardtii, and the freshwater green alga Chlorella vulgaris. The method is shown to be robust, highly reproducible, and fast, allowing for multiple samples to be analyzed throughout the time course of culturing, thus providing time-resolved information regarding lipid quantity and quality. Total time from harvesting to obtaining analytical results is less than 2h. © 2013.

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

PubMed

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical chains from self-assembly. The handedness of the twisted lamella can be determined by using rotation experiment of polarized light microscopy (PLM). Similar to the self-assembly of BCPs*, the examined results suggest the homochiral evolution in the crystallized chiral polylactides. The results presented in this Account demonstrate the notable progress in the spectral and morphological determination for the examination of molecular, conformational, and hierarchical chirality in self-assembled twisted superstructures of chiral polymers and helical phases of block copolymers and suggest the attainability of homochiral evolution in the self-assembly of chiral homopolymers and BCPs*. The suggested methodologies for the understanding of the mechanisms of the chirality transfer at different length scales provide the approaches to give Supporting Information for disclosing the mysteries of the homochiral evolution from molecular level.

Side-chain-side-chain interactions and stability of the helical state

NASA Astrophysics Data System (ADS)

Zangi, Ronen

2014-01-01

Understanding the driving forces that lead to the stability of the secondary motifs found in proteins, namely α-helix and β-sheet, is a major goal in structural biology. The thermodynamic stability of these repetitive units is a result of a delicate balance between many factors, which in addition to the peptide chain involves also the solvent. Despite the fact that the backbones of all amino acids are the same (except of that of proline), there are large differences in the propensity of the different amino acids to promote the helical structure. In this paper, we investigate by explicit-solvent molecular dynamics simulations the role of the side chains (modeled as coarse-grained single sites) in stabilizing α helices in an aqueous solution. Our model systems include four (six-mer-nine-mer) peptide lengths in which the magnitude of the effective attraction between the side chains is systematically increased. We find that these interactions between the side chains can induce (for the nine-mer almost completely) a transition from a coil to a helical state. This transition is found to be characterized by three states in which the intermediate state is a partially folded α-helical conformation. In the absence of any interactions between the side chains the free energy change for helix formation has a small positive value indicating that favorable contributions from the side chains are necessary to stabilize the helical conformation. Thus, the helix-coil transition is controlled by the effective potentials between the side-chain residues and the magnitude of the required attraction per residue, which is on the order of the thermal energy, reduces with the length of the peptide. Surprisingly, the plots of the population of the helical state (or the change in the free energy for helix formation) as a function of the total effective interactions between the side chains in the helical state for all peptide lengths fall on the same curve.

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

PubMed

Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M

2017-08-01

Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

Investigation of the Binding Interaction of Fatty Acids with Human G Protein-Coupled Receptor 40 Using a Site-Specific Fluorescence Probe by Flow Cytometry.

PubMed

Ren, Xiao-Min; Cao, Lin-Ying; Zhang, Jing; Qin, Wei-Ping; Yang, Yu; Wan, Bin; Guo, Liang-Hong

2016-04-05

Human G protein-coupled receptor 40 (hGPR40), with medium- and long-chain free fatty acids (FFAs) as its natural ligands, plays an important role in the enhancement of glucose-dependent insulin secretion. To date, information about the direct binding of FFAs to hGPR40 is very limited, and how carbon-chain length affects the activities of FFAs on hGPR40 is not yet understood. In this study, a fluorescein-fasiglifam analogue (F-TAK-875A) conjugate was designed and synthesized as a site-specific fluorescence probe to study the interaction of FFAs with hGPR40. hGPR40 was expressed in human embryonic kidney 293 cells and labeled with F-TAK-875A. By using flow cytometry, competitive binding of FFA and F-TAK-875A to hGPR40-expressed cells was measured. Binding affinities of 18 saturated FFAs, with carbon-chain lengths ranging from C6 to C23, were analyzed. The results showed that the binding potencies of FFAs to hGPR40 were dependent on carbon length. There was a positive correlation between length and binding potency for seven FFAs (C9-C15), with myristic acid (C15) showing the highest potency, 0.2% relative to TAK-875. For FFAs with a length of fewer than C9 or more than C15, they had very weak or no binding. Molecular docking results showed that the binding pocket of TAK-875 in hGPR40 could enclose FFAs with lengths of C15 or fewer. However, for FFAs with lengths longer than C15, part of the alkyl chain extended out of the binding pocket. This study provided insights into the structural dependence of FFAs binding to and activation of hGPR40.

Influence of in situ progressive N-terminal is still controversial truncation of glycogen branching enzyme in Escherichia coli DH5α on glycogen structure, accumulation, and bacterial viability.

PubMed

Wang, Liang; Regina, Ahmed; Butardo, Vito M; Kosar-Hashemi, Behjat; Larroque, Oscar; Kahler, Charlene M; Wise, Michael J

2015-05-07

Glycogen average chain length (ACL) has been linked with bacterial durability, but this was on the basis of observations across different species. We therefore wished to investigate the relationship between bacterial durability and glycogen ACL by varying glycogen average chain length in a single species. It has been shown that progressive shortening of the N-terminus of glycogen branching enzyme (GBE) leads to a lengthening of oligosaccharide inter-α-1,6-glycosidic chain lengths, so we sought to harness this to create a set of Escherichia coli DH5α strains with a range of glycogen average chain lengths, and assess these strains for durability related attributes, such as starvation, cold and desiccation stress resistance, and biofilm formation. A series of Escherichia coli DH5α mutants were created with glgB genes that were in situ progressively N-terminus truncated. N-terminal truncation shifted the distribution of glycogen chain lengths from 5-11 DP toward 13-50 DP, but the relationship between glgB length and glycogen ACL was not linear. Surprisingly, removal of the first 270 nucleotides of glgB (glgBΔ270) resulted in comparatively high glycogen accumulation, with the glycogen having short ACL. Complete knockout of glgB led to the formation of amylose-like glycogen containing long, linear α1,4-glucan chains with significantly reduced branching frequency. Physiologically, the set of mutant strains had reduced bacterial starvation resistance, while minimally increasing bacterial desiccation resistance. Finally, although there were no obvious changes in cold stress resistance or biofilm forming ability, one strain (glgBΔ180) had significantly increased biofilm formation in favourable media. Despite glgB being the first gene of an operon, it is clear that in situ mutation is a viable means to create more biologically relevant mutant strains. Secondly, there was the suggestion in the data that impairments of starvation, cold and desiccation resistance were worse for the strain lacking glgB, though the first of these was not statistically significant. The results provide prima facie evidence linking abiotic stress tolerance with shorter glycogen ACL. However, further work needs to be done, perhaps in a less labile species. Further work is also required to tease out the complex relationship between glycogen abundance and glycogen structure.

Correlation functions of main-chain polymer nematics constrained by tensorial and vectorial conservation laws

NASA Astrophysics Data System (ADS)

Svenšek, Daniel; Podgornik, Rudolf

2015-09-01

We present and analyze correlation functions of a main-chain polymer nematic in a continuum worm-like chain description for two types of constraints formalized by the tensorial and vectorial conservation laws, both originating in the microscopic chain integrity, i.e., the connectivity of the polymer chains. In particular, our aim is to identify the features of the correlation functions that are most susceptible to the differences between the two constraints. Besides the density and director autocorrelations in both the tensorial and vectorial cases, we calculate also the density-director correlation functions, the latter being a direct signature of the presence of a specific constraint. Its amplitude is connected to the strength of the constraint and is zero if none of the constraints are present, i.e., for a standard non-polymeric nematic. Generally, the correlation functions with the constraints differ substantially from the correlation functions in the non-polymeric case, if the constraints are strong which in practice requires long chains. Moreover, for the tensorial conservation law to be well distinguishable from the vectorial one, the chain persistence length should be much smaller than the total length of the chain, so that hairpins (chain backfolding) are numerous and the polar order is small.

Molecular structure of starches from maize mutants deficient in starch synthase III.

PubMed

Zhu, Fan; Bertoft, Eric; Källman, Anna; Myers, Alan M; Seetharaman, Koushik

2013-10-16

Molecular structures of starches from dull1 maize mutants deficient in starch synthase III (SSIII) with a common genetic background (W64A) were characterized and compared with the wild type. Amylose content with altered structure was higher in the nonwaxy mutants (25.4-30.2%) compared to the wild type maize (21.5%) as revealed by gel permeation chromatography. Superlong chains of the amylopectin component were found in all nonwaxy samples. Unit chain length distribution of amylopectins and their φ,β-limit dextrins (reflecting amylopectin internal structure) from dull1 mutants were also characterized by anion-exchange chromatography after debranching. Deficiency of SSIII led to an increased amount of short chains (DP ≤36 in amylopectin), whereas the content of long chains decreased from 8.4% to between 3.1 and 3.7% in both amylopectin and φ,β-limit dextrins. Moreover, both the external and internal chain lengths decreased, suggesting a difference in their cluster structures. Whereas the molar ratio of A:B-chains was similar in all samples (1.1-1.2), some ratios of chain categories were affected by the absence of SSIII, notably the ratio of "fingerprint" A-chains to "clustered" A-chains. This study highlighted the relationship between SSIII and the internal molecular structure of maize starch.

Diffusion on an Ising chain with kinks

NASA Astrophysics Data System (ADS)

Hamma, Alioscia; Mansour, Toufik; Severini, Simone

2009-07-01

We count the number of histories between the two degenerate minimum energy configurations of the Ising model on a chain, as a function of the length n and the number d of kinks that appear above the critical temperature. This is equivalent to count permutations of length n avoiding certain subsequences depending on d. We give explicit generating functions and compute the asymptotics. The setting considered has a role when describing dynamics induced by quantum Hamiltonians with deconfined quasi-particles.

The dynamics of complex formation between amylose brushes on gold and fatty acids by QCM-D.

PubMed

Cao, Zheng; Tsoufis, Theodoros; Svaldo-Lanero, Tiziana; Duwez, Anne-Sophie; Rudolf, Petra; Loos, Katja

2013-10-14

Amylose brushes were synthesized by enzymatic polymerization with glucose-1-phosphate as monomer and rabbit muscle phosphorylase b as catalyst on gold-covered surfaces of a quartz crystal microbalance. Fourier transform infrared (FT-IR) spectra confirmed the presence of the characteristic absorption peaks of amylose between 3100 cm(-1) and 3500 cm(-1). The thickness of the amylose brushes-measured by Spectroscopic Ellipsometry--can be tailored from 4 to 20 nm, depending on the reaction time. The contour length of the stretched amylose chains on gold surfaces has been evaluated by single molecule force spectroscopy, and a total chain length of about 20 nm for 16.2 nm thick amylose brushes was estimated. X-ray photoelectron spectroscopy (XPS) was employed to characterize the amylose brushes before and after the adsorption of fatty acids. The dynamics of inclusion complex formation between amylose brushes and two fatty acids (octanoic acid and myristic acid) with different chain length was investigated as a function of time using a quartz crystal microbalance with dissipation monitoring (QCM-D) immersed in the liquid phase. QCM-D signals including the frequency and dissipation shifts elucidated the effects of the fatty acid concentration, the solvent types, the chain length of the fatty acids and the thickness of the amylose brushes on the dynamics of fatty acid molecule adsorption on the amylose brush-modified sensor surfaces.

Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase.

PubMed

Jing, Fuyuan; Zhao, Le; Yandeau-Nelson, Marna D; Nikolau, Basil J

2018-02-28

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate's acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of the ACP moiety. Mutagenesis of residues within these two groups results in distinct synthetic acyl-ACP TEs that efficiently hydrolyze substrates with even shorter chains (C4- to C8-ACPs). These insights into structural determinants of acyl-ACP TE substrate specificity are useful in modifying this enzyme for tailored fatty acid production in engineered organisms.

Chondroitin sulfate synthase-2 is necessary for chain extension of chondroitin sulfate but not critical for skeletal development.

PubMed

Ogawa, Hiroyasu; Hatano, Sonoko; Sugiura, Nobuo; Nagai, Naoko; Sato, Takashi; Shimizu, Katsuji; Kimata, Koji; Narimatsu, Hisashi; Watanabe, Hideto

2012-01-01

Chondroitin sulfate (CS) is a linear polysaccharide consisting of repeating disaccharide units of N-acetyl-D-galactosamine and D-glucuronic acid residues, modified with sulfated residues at various positions. Based on its structural diversity in chain length and sulfation patterns, CS provides specific biological functions in cell adhesion, morphogenesis, neural network formation, and cell division. To date, six glycosyltransferases are known to be involved in the biosynthesis of chondroitin saccharide chains, and a hetero-oligomer complex of chondroitin sulfate synthase-1 (CSS1)/chondroitin synthase-1 and chondroitin sulfate synthase-2 (CSS2)/chondroitin polymerizing factor is known to have the strongest polymerizing activity. Here, we generated and analyzed CSS2(-/-) mice. Although they were viable and fertile, exhibiting no overt morphological abnormalities or osteoarthritis, their cartilage contained CS chains with a shorter length and at a similar number to wild type. Further analysis using CSS2(-/-) chondrocyte culture systems, together with siRNA of CSS1, revealed the presence of two CS chain species in length, suggesting two steps of CS chain polymerization; i.e., elongation from the linkage region up to Mr ∼10,000, and further extension. There, CSS2 mainly participated in the extension, whereas CSS1 participated in both the extension and the initiation. Our study demonstrates the distinct function of CSS1 and CSS2, providing a clue in the elucidation of the mechanism of CS biosynthesis.

Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of H(A) and B(A) cofactors.

PubMed

Saer, Rafael G; Hardjasa, Amelia; Rosell, Federico I; Mauk, A Grant; Murphy, Michael E P; Beatty, J Thomas

2013-04-02

In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion. The (M)L214 side chain was also replaced with Cys, Gln, and Asn to evaluate further the requirements for assembly of the RC with BChl in the HA pocket. Photoheterotrophic growth studies showed no difference in growth rates of the (M)214 nonpolar mutants at a low light intensity, but the growth of the amide-containing mutants was impaired. The absorbance spectra of purified RCs indicated that although absorbance changes are associated with the nonpolar mutations, the nonpolar mutant RC pigment compositions are the same as in the wild-type protein. Crystal structures of the (M)L214G, (M)L214A, and (M)L214N mutants were determined (determined to 2.2-2.85 Å resolution), confirming the presence of BPhe in the HA pocket and revealing alternative conformations of the phytyl tail of the accessory BChl in the BA site of these nonpolar mutants. Our results demonstrate that (i) BChl is converted to BPhe in a manner independent of the aliphatic side chain length of nonpolar residues replacing (M)214, (ii) BChl replaces BPhe if residue (M)214 has an amide-bearing side chain, (iii) (M)214 side chains containing sulfur are not sufficient to bind BChl in the HA pocket, and (iv) the (M)214 side chain influences the conformation of the phytyl tail of the BA BChl.

Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles.

PubMed

Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt

2015-12-28

The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs"-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.

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

Sun, Liang; Akgun, Bulent; Narayanan, Suresh

Swollen polymer brushes are found in many systems where the brush is intended to mediate interactions with the surroundings. The surface height fluctuations of planar polystyrene brushes (0.04 – 0.63 chains/nm2) highly swollen in toluene vapor are so strongly slowed by the tethering of the chains that they are unobservable in the current experimental window of length and time. This is the case despite the fact that the segmental dynamics of the brush chains should be very fast due to the substantial plasticization by the solvent. With respect to thermally stimulated fluctuations, the surfaces of these swollen brushes are solid-likemore » on time scales and length scales pertinent to many practical applications.« less

Small Angle Neutron Scattering Observation of Chain Retraction after a Large Step Deformation

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

Blanchard, A.; Heinrich, M.; Pyckhout-Hintzen, W.

The process of retraction in entangled linear chains after a fast nonlinear stretch was detected from time-resolved but quenched small angle neutron scattering (SANS) experiments on long, well-entangled polyisoprene chains. The statically obtained SANS data cover the relevant time regime for retraction, and they provide a direct, microscopic verification of this nonlinear process as predicted by the tube model. Clear, quantitative agreement is found with recent theories of contour length fluctuations and convective constraint release, using parameters obtained mainly from linear rheology. The theory captures the full range of scattering vectors once the crossover to fluctuations on length scales belowmore » the tube diameter is accounted for.« less

Communication disruption of guava moth (Coscinoptycha improbana) using a pheromone analog based on chain length.

PubMed

Suckling, D M; Dymock, J J; Park, K C; Wakelin, R H; Jamieson, L E

2013-09-01

The guava moth, Coscinoptycha improbana, an Australian species that infests fruit crops in commercial and home orchards, was first detected in New Zealand in 1997. A four-component pheromone blend was identified but is not yet commercially available. Using single sensillum recordings from male antennae, we established that the same olfactory receptor neurons responded to two guava moth sex pheromone components, (Z)-11-octadecen-8-one and (Z)-12-nonadecen-9-one, and to a chain length analog, (Z)-13-eicosen-10-one, the sex pheromone of the related peach fruit moth, Carposina sasakii. We then field tested whether this non-specificity of the olfactory neurons might enable disruption of sexual communication by the commercially available analog, using male catch to synthetic lures in traps in single-tree, nine-tree and 2-ha plots. A disruptive pheromone analog, based on chain length, is reported for the first time. Trap catches for guava moth were disrupted by three polyethylene tubing dispensers releasing the analog in single-tree plots (86% disruption of control catches) and in a plots of nine trees (99% disruption). Where peach fruit moth pheromone dispensers were deployed at a density of 1000/ha in two 2-ha areas, pheromone traps for guava moth were completely disrupted for an extended period (up to 470 days in peri-urban gardens in Mangonui and 422 days in macadamia nut orchards in Kerikeri). In contrast, traps in untreated areas over 100 m away caught 302.8 ± 128.1 moths/trap in Mangonui and 327.5 ± 78.5 moths/ trap in Kerikeri. The longer chain length in the pheromone analog has greater longevity than the natural pheromone due to its lower volatility. Chain length analogs may warrant further investigation for mating disruption in Lepidoptera, and screening using single-sensillum recording is recommended.

Helical Inversion of Gel Fibrils by Elongation of Perfluoroalkyl Chains as Studied by Vibrational Circular Dichroism.

PubMed

Sato, Hisako; Yajima, Tomoko; Yamagishi, Akihiko

2016-05-01

Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low-molecular mass weight gelator, N,N'-diperfluoroalkanoyl-1,2-trans-diaminocyclohexane. Attention was focused on the winding effects of (-CF2 )n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6-8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle-like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C-F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361-364, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Critical Role for Very-Long Chain Sphingolipids in Invariant Natural Killer T Cell Development and Homeostasis.

PubMed

Saroha, Ashish; Pewzner-Jung, Yael; Ferreira, Natalia S; Sharma, Piyush; Jouan, Youenn; Kelly, Samuel L; Feldmesser, Ester; Merrill, Alfred H; Trottein, François; Paget, Christophe; Lang, Karl S; Futerman, Anthony H

2017-01-01

The role of sphingolipids (SLs) in the immune system has come under increasing scrutiny recently due to the emerging contributions that these important membrane components play in regulating a variety of immunological processes. The acyl chain length of SLs appears particularly critical in determining SL function. Here, we show a role for very-long acyl chain SLs (VLC-SLs) in invariant natural killer T ( i NKT) cell maturation in the thymus and homeostasis in the liver. Ceramide synthase 2-null mice, which lack VLC-SLs, were susceptible to a hepatotropic strain of lymphocytic choriomeningitis virus, which is due to a reduction in the number of i NKT cells. Bone marrow chimera experiments indicated that hematopoietic-derived VLC-SLs are essential for maturation of i NKT cells in the thymus, whereas parenchymal-derived VLC-SLs are crucial for i NKT cell survival and maintenance in the liver. Our findings suggest a critical role for VLC-SL in i NKT cell physiology.

Strong-coupling phases of the spin-orbit-coupled spin-1 Bose-Hubbard chain: Odd-integer Mott lobes and helical magnetic phases

NASA Astrophysics Data System (ADS)

Pixley, J. H.; Cole, William S.; Spielman, I. B.; Rizzi, Matteo; Das Sarma, S.

2017-10-01

We study the odd-integer filled Mott phases of a spin-1 Bose-Hubbard chain and determine their fate in the presence of a Raman induced spin-orbit coupling which has been achieved in ultracold atomic gases; this system is described by a quantum spin-1 chain with a spiral magnetic field. The spiral magnetic field initially induces helical order with either ferromagnetic or dimer order parameters, giving rise to a spiral paramagnet at large field. The spiral ferromagnet-to-paramagnet phase transition is in a universality class with critical exponents associated with the divergence of the correlation length ν ≈2 /3 and the order-parameter susceptibility γ ≈1 /2 . We solve the effective spin model exactly using the density-matrix renormalization group, and compare with both a large-S classical solution and a phenomenological Landau theory. We discuss how these exotic bosonic magnetic phases can be produced and probed in ultracold atomic experiments in optical lattices.

Rheological properties in relation to molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2018-07-15

Quinoa starch granules are small (~0.5 - 3μm) with potentials for some food and other applications. To better exploit it as a new starch resource, this study investigates the steady shear and dynamic oscillatory properties of 9 quinoa starches varying in composition and structure. Steady shear analysis shows that the flow curves could be well described by 4 selected mathematic models. Temperature sweep analysis reveals that the quinoa starch encounters a 4-stage process including 2 phase transitions. Structure-function relationship analysis showed that composition as well as unit and internal chain length distribution of amylopectin have significant impact on the rheological properties (e.g., G' at 90°C) of quinoa starch. The roles of some individual unit chains and super-long unit chains of amylopectin in determining the rheological properties of quinoa starch were revealed. This study may stimulate further interest in understanding the structural basis of starch rheology. Copyright © 2018 Elsevier B.V. All rights reserved.

Influence of short chain organic acids and bases on the wetting properties and surface energy of submicrometer ceramic powders.

PubMed

Neirinck, Bram; Soccol, Dimitri; Fransaer, Jan; Van der Biest, Omer; Vleugels, Jef

2010-08-15

The effect of short chained organic acids and bases on the surface energy and wetting properties of submicrometer alumina powder was assessed. The surface chemistry of treated powders was determined by means of Diffuse Reflectance Infrared Fourier Transform spectroscopy and compared to untreated powder. The wetting of powders was measured using a modified Washburn method, based on the use of precompacted powder samples. The geometric factor needed to calculate the contact angle was derived from measurements of the porous properties of the powder compacts. Contact angle measurements with several probe liquids before and after modification allowed a theoretical estimation of the surface energy based on the surface tension component theory. Trends in the surface energy components were linked to observations in infrared spectra. The results showed that the hydrophobic character of the precompacted powder depends on both the chain length and polar group of the modifying agent. Copyright 2010 Elsevier Inc. All rights reserved.

KnotProt: a database of proteins with knots and slipknots

PubMed Central

Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I.

2015-01-01

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. PMID:25361973

Electrostatic effects on hyaluronic acid configuration

NASA Astrophysics Data System (ADS)

Berezney, John; Saleh, Omar

2015-03-01

In systems of polyelectrolytes, such as solutions of charged biopolymers, the electrostatic repulsion between charged monomers plays a dominant role in determining the molecular conformation. Altering the ionic strength of the solvent thus affects the structure of such a polymer. Capturing this electrostatically-driven structural dependence is important for understanding many biological systems. Here, we use single molecule manipulation experiments to collect force-extension behavior on hyaluronic acid (HA), a polyanion which is a major component of the extracellular matrix in all vertebrates. By measuring HA elasticity in a variety of salt conditions, we are able to directly assess the contribution of electrostatics to the chain's self-avoidance and local stiffness. Similar to recent results from our group on single-stranded nucleic acids, our data indicate that HA behaves as a swollen chain of electrostatic blobs, with blob size proportional to the solution Debye length. Our data indicate that the chain structure within the blob is not worm-like, likely due to long-range electrostatic interactions. We discuss potential models of this effect.

[Pea (Pisum sativum) genes, participating in symbiosis with nitrogen-fixing bacteria. III. Study of the structure of the ENOD12 early nodulin gene for various types of peas using the polymerase chain reaction (PCR)].

PubMed

Kozik, A V; Matvienko, M A; Men', A E; Zalenskiĭ, A O; Tikhonovich, I A

1992-01-01

We have determined the length of early noduline gene ENOD12 in various varieties and lines of pea (Pisum sativum) using the polymerase chain reaction (PCR). It was demonstrated that promoter regions of ENOD12A and ENOD12B genes in line 2150 (Afghanistan) are longer than these in variety "Feltham first". The disparity is 14 bp. When studying these genes in 7 different lines and varieties of pea it was found that ENOD12A gene is more variable in size than the ENOD12B gene. We showed the possibility to analyze the heritage of ENOD12 gene's alleles by using the PCR method.

End product yields from the extraruminal fermentation of various polysaccharide, protein and nucleic acid components of biofuels feedstocks.

PubMed

Weimer, Paul J

2011-02-01

"Extraruminal" fermentations employing in vitro incubation of mixed ruminal bacterial consortia, are capable of converting a complex array of biomass materials to mixtures of volatile fatty acids (VFA), methane, and carbon dioxide. Most of the potential energy in the biomass feedstock is retained in the VFA products, which are potential reactants for electrochemical conversion to hydrocarbon fuels. Quantitative data on VFA yields and proportions from biomass components are necessary for determining industrial feasibility, but such measurements have not been systematically reported. VFA yields and proportions were determined for a variety of carbohydrates, proteins and nucleic acids. Carbohydrates yielded primarily acetic and propionic acids, while proteins also yielded a more favorable product mix (longer average chain length and branched chain VFAs). Addition of certain co-substrates (e.g., glycerol) favorably improved the VFA product mix. The results have implications for hydrocarbon fuel generation from biomass materials by hybrid fermentation/chemical processes. Published by Elsevier Ltd.

Molecular Modeling of Thermosetting Polymers: Effects of Degree of Curing and Chain Length on Thermo-Mechanical Properties

DTIC Science & Technology

2012-08-01

paper, we will first briefly discuss our recent results, using coarse-grained bead - spring model , on the dependence of failure stress and failure...length of the resin strands. In the coarse-grained model used here the polymer network is treated as a bead - spring system. To create highly cross...simulations of Thermosets We have used a coarse-grained bead - spring model to study the dependence of the mechanical properties of thermosets on chain

Surface monolayers of well-defined amphiphilic block copolymer composed of poly(acrylic acid) or poly(oxyethylene) and poly(styrene). Interpolymer complexation at the air-water interface

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

Niwa, Masazo; Hayashi, Takehiro; Higashi, Nobuyuki

1990-01-01

Amphiphilic block polymers (2,3) composed of poly(acrylic acid) (PAA) or poly(oxyethylene) (POE) and chain length controlled poly(styrene) (PSt) have been prepared by using a catalytic system of tribromomethyl-terminated oligomer and manganese carbonyl. All the amphiphilic materials formed well-behaved surface monolayers, and the II-A curves for them expanded systematically with an increase of the PSt chain length.

Non-surface activity and micellization behavior of cationic amphiphilic block copolymer synthesized by reversible addition-fragmentation chain transfer process.

PubMed

Ghosh, Arjun; Yusa, Shin-ichi; Matsuoka, Hideki; Saruwatari, Yoshiyuki

2011-08-02

Cationic amphiphilic diblock copolymers of poly(n-butylacrylate)-b-poly(3-(methacryloylamino)propyl)trimethylammonium chloride) (PBA-b-PMAPTAC) with various hydrophobic and hydrophilic chain lengths were synthesized by a reversible addition-fragmentation chain transfer (RAFT) process. Their molecular characteristics such as surface activity/nonactivity were investigated by surface tension measurements and foam formation observation. Their micelle formation behavior and micelle structure were investigated by fluorescence probe technique, static and dynamic light scattering (SLS and DLS), etc., as a function of hydrophilic and hydrophobic chain lengths. The block copolymers were found to be non-surface active because the surface tension of the aqueous solutions did not change with increasing polymer concentration. Critical micelle concentration (cmc) of the polymers could be determined by fluorescence and SLS measurements, which means that these polymers form micelles in bulk solution, although they were non-surface active. Above the cmc, the large blue shift of the emission maximum of N-phenyl-1-naphthylamine (NPN) probe and the low micropolarity value of the pyrene probe in polymer solution indicate the core of the micelle is nonpolar in nature. Also, the high value of the relative intensity of the NPN probe and the fluorescence anisotropy of the 1,6-diphenyl-1,3,5-hexatriene (DPH) probe indicated that the core of the micelle is highly viscous in nature. DLS was used to measure the average hydrodynamic radii and size distribution of the copolymer micelles. The copolymer with the longest PBA block had the poorest water solubility and consequently formed micelles with larger size while having a lower cmc. The "non-surface activity" was confirmed for cationic amphiphilic diblock copolymers in addition to anionic ones studied previously, indicating the universality of non-surface activity nature.

End-monomer Dynamics in Semiflexible Polymers

PubMed Central

Hinczewski, Michael; Schlagberger, Xaver; Rubinstein, Michael; Krichevsky, Oleg; Netz, Roland R.

2009-01-01

Spurred by an experimental controversy in the literature, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations and dynamic mean-field theory. Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) 〈r2(t)〉 ~ t1/2 at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling 〈r2(t)〉 ~ t2/3 in the same time range. Using hydrodynamic simulations, analytical and scaling theories, we find a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, α(t) = d log〈r2(t)〉/d log t, drops below the Zimm value of 2/3 for sufficiently long chains. The deviation from the Zimm prediction increases with chain length, though it does not reach the Rouse limit of 1/2. The qualitative features of this intermediate regime, found in simulations and in an improved mean-field theory for semiflexible polymers, in particular the variation of α(t) with chain and persistence lengths, can be reproduced through a heuristic scaling argument. Anomalously low values of the effective exponent α are explained by hydrodynamic effects related to the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger length scales. PMID:21359118

VeA of Aspergillus niger increases spore dispersing capacity by impacting conidiophore architecture.

PubMed

Wang, Fengfeng; Dijksterhuis, Jan; Wyatt, Timon; Wösten, Han A B; Bleichrodt, Robert-Jan

2015-01-01

Aspergillus species are highly abundant fungi worldwide. Their conidia are among the most dominant fungal spores in the air. Conidia are formed in chains on the vesicle of the asexual reproductive structure called the conidiophore. Here, it is shown that the velvet protein VeA of Aspergillus niger maximizes the diameter of the vesicle and the spore chain length. The length and width of the conidiophore stalk and vesicle were reduced nearly twofold in a ΔveA strain. The latter implies a fourfold reduced surface area to develop chains of spores. Over and above this, the conidial chain length was approximately fivefold reduced. The calculated 20-fold reduction in formation of conidia by ΔveA fits the 8- to 17-fold decrease in counted spore numbers. Notably, morphology of the ΔveA conidiophores of A. niger was very similar to that of wild-type Aspergillus sydowii. This suggests that VeA is key in conidiophore architecture diversity in the fungal kingdom. The finding that biomass formation of the A. niger ΔveA strain was reduced twofold shows that VeA not only impacts dispersion capacity but also colonization capacity of A. niger.

Dynamics and order-disorder transitions in bidisperse diblock copolymer blends

NASA Astrophysics Data System (ADS)

Wang, Yueqiang; Li, Xuan; Tang, Ping; Yang, Yuliang

2011-03-01

We employ the dynamic extension of self-consistent field theory (DSCFT) to study dynamics and order-disorder transitions (ODT) in AB diblock copolymer binary mixtures of two different monodisperse chain lengths by imitating the dynamic storage modulus G‧ corresponding to any given morphology in the oscillatory shear measurements. The different polydispersity index (PDI) is introduced by binary blending AB diblock copolymers with variations in chain lengths and chain number fractions. The simulation results show that the increase of polydispersity in the minority or symmetric block introduces a decrease in the segregation strength at the ODT, ( χN) ODT, whereas the increase of polydispersity in the majority block results in a decrease, then increase and final decrease again in ( χN) ODT. To the best of our knowledge, our DSCFT simulations, for the first time, predict an increase in ( χN) ODT with the PDI in the majority block, which produces the experimental results. The simulations by previous SCFT, which generally speaking, is capable of describing equilibrium morphologies, however, contradict the experimental data. The polydispersity acquired by properly tuning the chain lengths and number fractions of binary diblock copolymer blends should be a convenient and efficient way to control the microphase separation strength at the ODT.

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

PubMed

Nakamura, Issei

2014-05-29

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Newtonian Analysis of a Folded Chain Drop

ERIC Educational Resources Information Center

Mungan, Carl E.

2018-01-01

Consider a chain of length L that hangs in a U shape with end A fixed to a rigid support and free end E released from rest starting from the same initial height (call it y = 0) as A. Figure 1 sketches the chain after end E has fallen a distance y. Points O and A are assumed to be close enough to each other and the chain flexible enough that the…

Collapse kinetics of vibrated granular chains

NASA Astrophysics Data System (ADS)

Jeng, Pei-Ren; Chen, Kuan Hua; Hwang, Gwo-jen; Lien, Chenhsin; To, Kiwing; Chou, Y. C.

2011-12-01

The kinetics of the collapse of the coil state into condensed states is studied with vibrated granular chain composed of N metal beads partially immersed in water. The radius of gyration of the chain, Rg is measured. For short chains (N < 140), disk-like condensed state is formed and Rg decreases with time such that the function ΔRg2 (≡ Rg2 - Rg2(∞)) = A e-t/τ, where the relaxation time τ follows a power-law dependence on the chain length N with an exponent γ = 1.9 ± 0.2. For the chains with length N ≥ 300, rod-like clusters are observed during the initial stage of collapse and Rg2 = Rg2(0) - Btβ, with β = 0.6 ± 0.1. In the coarsening stage, the exponential dependence of ΔRg2 on time still holds, however, the relaxation time τ fluctuates and has no simple dependence on N. Furthermore, the time dependence of the averaged radius of gyration of the individual clusters, Rg,cl can be described by the theory of Lifshitz and Slyozov. A peak in the structure function of long chains is observed in the initial stage of the collapse transition. The collapse transition in the bead chains is a first order phase transition. However, features of the spinodal decomposition are also observed.

The Impact of Ownership on Hospice Service Use, 2005–2011

PubMed Central

Stevenson, David G.; Grabowski, David C.; Keating, Nancy L.; Huskamp, Haiden A.

2016-01-01

Background/Objectives For-profit agencies comprise the majority of all United States hospice agencies, prompting concerns about aggressive enrollment practices and deficient care. Using detailed administrative data from 2005–2011, we sought to assess differences in patient populations and service use by hospice ownership, chain status, and agency size. Design/Participants Retrospective cohort study of 5,405,526 Medicare beneficiaries age 65+ enrolled in hospice during 2005–2011. Hospice use by ownership category (for-profit non-chain and chain, not-for-profit non-chain and chain, government) and agency size (0–50 patients, 51–200, 201–400, 401+). Mean length-of-use, stays ≤3 days, stays ending with live discharge, and decedents receiving no general inpatient care (GIP) or continuous home care (CHC) level hospice in the last 7 days of life. Results After adjusting for patient and geographic differences, for-profit non-chain and chain agencies had longer mean lengths-of-use (84.5 and 91.2 days, respectively) than other agency types (66.3–72.5 days); higher rates of live discharge (21.0% and 20.2% versus 14.6%–15.9%); and lower proportions of stays of ≤3 days (13.9% and 14.7% versus 16.6%–17.5%) (all p-values<0.001). The proportion of decedents not receiving GIP/CHC level care before death was highest among for-profit chains (75.9%) and lowest among not-for-profit non-chains (63.2%). Across ownership categories, smaller agencies had longer mean lengths-of-use, higher live discharge rates, lower rates of stays ≤3 days, and higher rates of patients receiving no GIP/CHC level care. Considerable variation in patient traits and unadjusted service use existed among the nation’s largest chains. Conclusion Although for-profit and not-for-profit hospice agencies differ along key dimensions, our results convey substantial heterogeneity within these categories, highlighting the need to consider factors such as agency size and chain affiliation in understanding variations in Medicare beneficiaries’ hospice care. PMID:27131344

Is average chain length of plant lipids a potential proxy for vegetation, environment and climate changes?

NASA Astrophysics Data System (ADS)

Wang, M.; Zhang, W.; Hou, J.

2015-04-01

Average chain length (ACL) of leaf wax components preserved in lacustrine sediments and soil profiles has been widely adopted as a proxy indicator for past changes in vegetation, environment and climate during the late Quaternary. The fundamental assumption is that woody plants produce leaf waxes with shorter ACL values than non-woody plants. However, there is a lack of systematic survey of modern plants to justify the assumption. Here, we investigated various types of plants at two lakes, Blood Pond in the northeastern USA and Lake Ranwu on the southeastern Tibetan Plateau, and found that the ACL values were not significantly different between woody and non-woody plants. We also compiled the ACL values of modern plants in the literatures and performed a meta-analysis to determine whether a significant difference exists between woody and non-woody plants at single sites. The results showed that the ACL values of plants at 19 out of 26 sites did not show a significant difference between the two major types of plants. This suggests that extreme caution should be taken in using ACL as proxy for past changes in vegetation, environment and climate.

Structural insights into Cydia pomonella pheromone binding protein 2 mediated prediction of potentially active semiochemicals

NASA Astrophysics Data System (ADS)

Tian, Zhen; Liu, Jiyuan; Zhang, Yalin

2016-03-01

Given the advantages of behavioral disruption application in pest control and the damage of Cydia pomonella, due progresses have not been made in searching active semiochemicals for codling moth. In this research, 31 candidate semiochemicals were ranked for their binding potential to Cydia pomonella pheromone binding protein 2 (CpomPBP2) by simulated docking, and this sorted result was confirmed by competitive binding assay. This high predicting accuracy of virtual screening led to the construction of a rapid and viable method for semiochemicals searching. By reference to binding mode analyses, hydrogen bond and hydrophobic interaction were suggested to be two key factors in determining ligand affinity, so is the length of molecule chain. So it is concluded that semiochemicals of appropriate chain length with hydroxyl group or carbonyl group at one head tended to be favored by CpomPBP2. Residues involved in binding with each ligand were pointed out as well, which were verified by computational alanine scanning mutagenesis. Progress made in the present study helps establish an efficient method for predicting potentially active compounds and prepares for the application of high-throughput virtual screening in searching semiochemicals by taking insights into binding mode analyses.

Structural insights into Cydia pomonella pheromone binding protein 2 mediated prediction of potentially active semiochemicals

PubMed Central

Tian, Zhen; Liu, Jiyuan; Zhang, Yalin

2016-01-01

Given the advantages of behavioral disruption application in pest control and the damage of Cydia pomonella, due progresses have not been made in searching active semiochemicals for codling moth. In this research, 31 candidate semiochemicals were ranked for their binding potential to Cydia pomonella pheromone binding protein 2 (CpomPBP2) by simulated docking, and this sorted result was confirmed by competitive binding assay. This high predicting accuracy of virtual screening led to the construction of a rapid and viable method for semiochemicals searching. By reference to binding mode analyses, hydrogen bond and hydrophobic interaction were suggested to be two key factors in determining ligand affinity, so is the length of molecule chain. So it is concluded that semiochemicals of appropriate chain length with hydroxyl group or carbonyl group at one head tended to be favored by CpomPBP2. Residues involved in binding with each ligand were pointed out as well, which were verified by computational alanine scanning mutagenesis. Progress made in the present study helps establish an efficient method for predicting potentially active compounds and prepares for the application of high-throughput virtual screening in searching semiochemicals by taking insights into binding mode analyses. PMID:26928635

Mechanistic Design of Chemically Diverse Polymers with Applications in Oral Drug Delivery.

PubMed

Mosquera-Giraldo, Laura I; Borca, Carlos H; Meng, Xiangtao; Edgar, Kevin J; Slipchenko, Lyudmila V; Taylor, Lynne S

2016-11-14

Polymers play a key role in stabilizing amorphous drug formulations, a recent strategy employed to improve solubility and bioavailability of drugs delivered orally. However, the molecular mechanism of stabilization is unclear, therefore, the rational design of new crystallization-inhibiting excipients remains a substantial challenge. This article presents a combined experimental and computational approach to elucidate the molecular features that improve the effectiveness of cellulose polymers as solution crystallization inhibitors, a crucial first step toward their rational design. Polymers with chemically diverse substituents including carboxylic acids, esters, ethers, alcohols, amides, amines, and sulfides were synthesized. Measurements of nucleation induction times of the model drug, telaprevir, show that the only effective polymers contained carboxylate groups in combination with an optimal hydrocarbon chain length. Computational results indicate that polymer conformation as well as solvation free energy are important determinants of effectiveness at inhibiting crystallization and show that simulations are a promising predictive tool in the screening of polymers. This study suggests that polymers need to have an adequate hydrophilicity to promote solvation in an aqueous environment, and sufficient hydrophobic regions to drive interactions with the drug. Particularly, the right balance between key substituent groups and lengths of hydrocarbon side chains is needed to create effective materials.

Monosaccharides as Versatile Units for Water-Soluble Supramolecular Polymers.

PubMed

Leenders, Christianus M A; Jansen, Gijs; Frissen, Martijn M M; Lafleur, René P M; Voets, Ilja K; Palmans, Anja R A; Meijer, E W

2016-03-18

We introduce monosaccharides as versatile water-soluble units to compatibilise supramolecular polymers based on the benzene-1,3,5-tricarboxamide (BTA) moiety with water. A library of monosaccharide-based BTAs is evaluated, varying the length of the alkyl chain (hexyl, octyl, decyl and dodecyl) separating the BTA and saccharide units, as well as the saccharide units (α-glucose, β-glucose, α-mannose and α-galactose). In all cases, the monosaccharides impart excellent water compatibility. The length of the alkyl chain is the determining factor to obtain either long, one-dimensional supramolecular polymers (dodecyl spacer), small aggregates (decyl spacer) or molecularly dissolved (octyl and hexyl) BTAs in water. For the BTAs comprising a dodecyl spacer, our results suggest that a cooperative self-assembly process is operative and that the introduction of different monosaccharides does not significantly change the self- assembly behaviour. Finally, we investigate the potential of post-assembly functionalisation of the formed supramolecular polymers by taking advantage of dynamic covalent bond formation between the monosaccharides and benzoxaboroles. We observe that the supramolecular polymers readily react with a fluorescent benzoxaborole derivative permitting imaging of these dynamic complexes by confocal fluorescence microscopy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phytosphingosine, sphingosine and dihydrosphingosine ceramides in model skin lipid membranes: permeability and biophysics.

PubMed

Školová, Barbora; Kováčik, Andrej; Tesař, Ondřej; Opálka, Lukáš; Vávrová, Kateřina

2017-05-01

Ceramides based on phytosphingosine, sphingosine and dihydrosphingosine are essential constituents of the skin lipid barrier that protects the body from excessive water loss. The roles of the individual ceramide subclasses in regulating skin permeability and the reasons for C4-hydroxylation of these sphingolipids are not completely understood. We investigated the chain length-dependent effects of dihydroceramides, sphingosine ceramides (with C4-unsaturation) and phytoceramides (with C4-hydroxyl) on the permeability, lipid organization and thermotropic behavior of model stratum corneum lipid membranes composed of ceramide/lignoceric acid/cholesterol/cholesteryl sulfate. Phytoceramides with very long C24 acyl chains increased the permeability of the model lipid membranes compared to dihydroceramides or sphingosine ceramides with the same chain lengths. Either unsaturation or C4-hydroxylation of dihydroceramides induced chain length-dependent increases in membrane permeability. Infrared spectroscopy showed that C4-hydroxylation of the sphingoid base decreased the relative ratio of orthorhombic chain packing in the membrane and lowered the miscibility of C24 phytoceramide with lignoceric acid. The phase separation in phytoceramide membranes was confirmed by X-ray diffraction. In contrast, phytoceramides formed strong hydrogen bonds and highly thermostable domains. Thus, the large heterogeneity in ceramide structures and in their aggregation mechanisms may confer resistance towards the heterogeneous external stressors that are constantly faced by the skin barrier. Copyright © 2017 Elsevier B.V. All rights reserved.

Brownian Dynamics Simulations of Polyelectrolyte Adsorption in Shear Flow

NASA Astrophysics Data System (ADS)

Panwar, Ajay

2005-03-01

The adsorption of polyelectrolytes onto charged surfaces often occurs in microfludic devices and can influence their operation. We employ Brownian dynamics simulations to investigate the effect of a simple shear flow on the adsorption of an isolated polyelectrolyte molecule onto an oppositely charged surface. The polyelectrolyte is modeled as a freely-jointed bead-rod chain where the total charge is distributed uniformly among all the beads, and the beads are allowed to interact with one another and the charged surface through screened Coulombic interactions. The simulations are performed by placing the chain some distance above the surface, and the adsorption behavior is studied as a function of the screening length. Specifically, we look at the components of the radius of gyration, normal and parallel to the adsorbing surface, as functions of the screening length, both in the absence and presence of the flow. We find that in the absence of flow, the chain lies flat and stretched on the adsorbing surface in the limit of weak screening, but attains free solution behavior in the limit of strong screening. In the presence of a shear flow, the chain orientation in the direction of the flow increases with increasing Weissenberg number over the entire range of screening lengths studied. We also find that increasing the strength of the shear flow leads to an increased contact of the chain with the surface compared to the case when no flow is present.

Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic.

PubMed

Bai, Xin; Tang, Kujin; Ren, Jie; Waterman, Michael; Sun, Fengzhu

2017-10-03

Alignment-free sequence comparison using counts of word patterns (grams, k-tuples) has become an active research topic due to the large amount of sequence data from the new sequencing technologies. Genome sequences are frequently modelled by Markov chains and the likelihood ratio test or the corresponding approximate χ 2 -statistic has been suggested to compare two sequences. However, it is not known how to best choose the word length k in such studies. We develop an optimal strategy to choose k by maximizing the statistical power of detecting differences between two sequences. Let the orders of the Markov chains for the two sequences be r 1 and r 2 , respectively. We show through both simulations and theoretical studies that the optimal k= max(r 1 ,r 2 )+1 for both long sequences and next generation sequencing (NGS) read data. The orders of the Markov chains may be unknown and several methods have been developed to estimate the orders of Markov chains based on both long sequences and NGS reads. We study the power loss of the statistics when the estimated orders are used. It is shown that the power loss is minimal for some of the estimators of the orders of Markov chains. Our studies provide guidelines on choosing the optimal word length for the comparison of Markov sequences.

Computer Simulations of Bottlebrush Melts and Soft Networks

NASA Astrophysics Data System (ADS)

Cao, Zhen; Carrillo, Jan-Michael; Sheiko, Sergei; Dobrynin, Andrey

We have studied dense bottlebrush systems in a melt and network state using a combination of the molecular dynamics simulations and analytical calculations. Our simulations show that the bottlebrush macromolecules in a melt behave as ideal chains with the effective Kuhn length bK. The bottlebrush induced bending rigidity is due to redistribution of the side chains upon backbone bending. Kuhn length of the bottlebrushes increases with increasing the side-chain degree of polymerization nsc as bK ~nsc0 . 46 . This model of bottlebrush macromolecules is extended to describe mechanical properties of bottlebrush networks in linear and nonlinear deformation regimes. In the linear deformation regime, the network shear modulus scales with the degree of polymerization of the side chains as G0 ~nsc + 1 - 1 as long as the ratio of the Kuhn length to the size of the fully extended bottlebrush backbone between crosslinks, Rmax, is smaller than unity, bK /Rmax < < 1 . Bottlebrush networks with bK /Rmax ~ 1 demonstrate behavior similar to that of networks of semiflexible chains with G0 ~nsc- 0 . 5 . In the nonlinear deformation regime, the deformation dependent shear modulus is a universal function of the first strain invariant I1 and bottlebrush backbone deformation ratio β describing stretching ability of the bottlebrush backbone between crosslinks. Nsf DMR-1409710 DMR-1436201.

Primary alcohols activate human TRPA1 channel in a carbon chain length-dependent manner.

PubMed

Komatsu, Tomoko; Uchida, Kunitoshi; Fujita, Fumitaka; Zhou, Yiming; Tominaga, Makoto

2012-04-01

Transient receptor potential ankyrin 1 (TRPA1) is a calcium-permeable non-selective cation channel that is mainly expressed in primary nociceptive neurons. TRPA1 is activated by a variety of noxious stimuli, including cold temperatures, pungent compounds such as mustard oil and cinnamaldehyde, and intracellular alkalization. Here, we show that primary alcohols, which have been reported to cause skin, eye or nasal irritation, activate human TRPA1 (hTRPA1). We measured intracellular Ca(2+) changes in HEK293 cells expressing hTRPA1 induced by 1 mM primary alcohols. Higher alcohols (1-butanol to 1-octanol) showed Ca(2+) increases proportional to the carbon chain length. In whole-cell patch-clamp recordings, higher alcohols (1-hexanol to 1-octanol) activated hTRPA1 and the potency increased with the carbon chain length. Higher alcohols evoked single-channel opening of hTRPA1 in an inside-out configuration. In addition, cysteine at 665 in the N terminus and histidine at 983 in the C terminus were important for hTRPA1 activation by primary alcohols. Furthermore, straight-chain secondary alcohols increased intracellular Ca(2+) concentrations in HEK293 cells expressing hTRPA1, and both primary and secondary alcohols showed hTRPA1 activation activities that correlated highly with their octanol/water partition coefficients. On the other hand, mouse TRPA1 did not show a strong response to 1-hexanol or 1-octanol, nor did these alcohols evoke significant pain in mice. We conclude that primary and secondary alcohols activate hTRPA1 in a carbon chain length-dependent manner. TRPA1 could be a sensor of alcohols inducing skin, eye and nasal irritation in human.

Rotational dynamics of coumarin-153 and 4-aminophthalimide in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: effect of alkyl chain length on the rotational dynamics.

PubMed

Das, Sudhir Kumar; Sarkar, Moloy

2012-01-12

Rotational dynamics of two neutral organic solutes, coumarin-153 (C-153) and 4-aminophthalimide (AP), with only the latter having hydrogen-bond-donating ability, has been investigated in a series of 1-ethyl-3-methylimidazolium alkyl sulfate ionic liquids as a function of temperature. The ionic liquids differ only in the length of the linear alkyl side chain (alkyl = ethyl, butyl, hexyl, and octyl) on the anionic moiety. The present study has been undertaken to examine the role of alkyl side chains on the rotational dynamics of the two solutes in these ionic liquids. Analysis of the results using Stokes-Einstein-Debye hydrodynamic theory indicates that the rotational dynamics of C-153 lies between the stick and slip boundary condition in the ethyl analogue and finally reaches subslip condition as in case of the octyl substituent. The observed rotational behavior of C-153 has been explained on the basis of an increase in the size of the solvent, which offers lower friction for solute rotation. On the other hand, AP shows superstick behavior in the ethyl system and exceeds the stick limit in the octyl derivative. Superstick behavior of AP has been attributed to the specific hydrogen-bonding interaction between AP and the sulfate moiety. Proton NMR investigation confirms the hydrogen-bonding interaction between the N-H hydrogen of AP and the ionic liquid. The decrease in rotational coupling constant values for AP with increasing length of alkyl side chains has been attributed to the decrease in the solute-solvent-specific interaction with an increase in the alkyl side chain length on the sulfate moiety.

Toxicity evaluation of selected ammonium-based ionic liquid forms with MCPP and dicamba moieties on Pseudomonas putida.

PubMed

Piotrowska, Aleksandra; Syguda, Anna; Wyrwas, Bogdan; Chrzanowski, Łukasz; Heipieper, Hermann J

2017-01-01

Combination of the hydrophilic herbicidal anion with hydrophobic, antimicrobial ammonium cation allows to obtain compounds in ionic liquid form with better properties then conventional herbicides. Both cation and anion can be modified by selection of herbicide and the length of alkyl chains in cation structure. However the knowledge of their potential toxic effects are still limited. Furthermore, the relation between hydrophobicity associated with the length of alkyl chains and toxicity for ionic liquids has not been thoroughly studied. Therefore we investigated toxic effects of herbicidal ionic liquid forms on growth inhibition, given as EC 50, of the common soil bacterium Pseudomonas putida. We thereby concentrated on quaternary ammonium salts. Analyzed compounds were composed of dicamba or MCPP moieties and cation with various alkyl chain lengths (n = 6,8,10) We compared them with commercial herbicides, and ammonium-based ionic liquids with neutral anion (Br - ). In addition, cis-trans isomerisation of unsaturated membrane fatty acids in Pseudomonas putida was applied as the proxy for toxicity and membrane activity. We showed that toxicity increased with the length of alkyl chains. However, this correlation is only valid for six and eight carbon atom in alkyl chains, where for n = 10 the EC 50 values rise by one order of magnitude. In our studies, the herbicidal ionic liquids [C 10 ,C 10 ,C 1 ,C 1 N][MCPP] and [C 10 ,C 10 ,C 1 ,C 1 N][dicamba] showed the lowest toxicity among analyzed quaternary ammonium salts and comparable toxicity with corresponding herbicides. No clear increase in toxicity could be followed by changing the anion moieties for ammonium-based ionic liquid forms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Importance of the residue Asp 290 on chain length selectivity and catalytic efficiency of recombinant Staphylococcus simulans lipase expressed in E. coli.

PubMed

Sayari, Adel; Mosbah, Habib; Gargouri, Youssef

2007-05-01

In addition to their physiological importance, microbial lipases, like staphylococcal ones, are of considerable commercial interest for biotechnological applications such as detergents, food production, and pharmaceuticals and industrial synthesis of fine chemicals. The gene encoding the extracellular lipase of Staphylococcus simulans (SSL) was subcloned in the pET-14b expression vector and expressed in Esherichia coli BL21 (DE3). The wild-type SSL was expressed as amino terminal His6-tagged recombinant protein. One-step purification of the recombinant lipase was achieved with nickel metal affinity column. The purified His-tagged SSL (His6-SSL) is able to hydrolyse triacylglycerols without chain length selectivity. The major differences among lipases are reflected in their chemical specificity in the hydrolysis of peculiar ester bonds, and their respective capacity to hydrolyse substrates having different physico-chemical properties. It has been proposed, using homology alignment, that the region around the residue 290 of Staphylococcus hyicus lipase could be involved in the selection of the substrate. To evaluate the importance of this environment, the residue Asp290 of Staphylococcus simulans lipase was mutated to Ala using site-directed mutagenesis. The mutant expression plasmid was also overexpressed in Esherichia coli and purified with a nickel metal affinity column. The substitution of Asp290 by Ala was accompanied by a significant shift of the acyl-chain length specificity of the mutant towards short chain fatty acid esters. Kinetic studies of wild-type SSL and its mutant D290A were carried out, and show essentially that the catalytic efficiency (k cat /K M ) of the mutant was affected. Our results confirmed that Asp290 is important for the chain length selectivity and catalytic efficiency of Staphylococcus simulans lipase.

Permeability of acetic acid across gel and liquid-crystalline lipid bilayers conforms to free-surface-area theory.

PubMed Central

Xiang, T X; Anderson, B D

1997-01-01

Solubility-diffusion theory, which treats the lipid bilayer membrane as a bulk lipid solvent into which permeants must partition and diffuse across, fails to account for the effects of lipid bilayer chain order on the permeability coefficient of any given permeant. This study addresses the scaling factor that must be applied to predictions from solubility-diffusion theory to correct for chain ordering. The effects of bilayer chemical composition, temperature, and phase structure on the permeability coefficient (Pm) of acetic acid were investigated in large unilamellar vesicles by a combined method of NMR line broadening and dynamic light scattering. Permeability values were obtained in distearoylphosphatidylcholine, dipalmitoylphosphatidylcholine, dimyristoylphosphatidylcholine, and dilauroylphosphatidylcholine bilayers, and their mixtures with cholesterol, at various temperatures both above and below the gel-->liquid-crystalline phase transition temperatures (Tm). A new scaling factor, the permeability decrement f, is introduced to account for the decrease in permeability coefficient from that predicted by solubility-diffusion theory owing to chain ordering in lipid bilayers. Values of f were obtained by division of the observed Pm by the permeability coefficient predicted from a bulk solubility-diffusion model. In liquid-crystalline phases, a strong correlation (r = 0.94) between f and the normalized surface density sigma was obtained: in f = 5.3 - 10.6 sigma. Activation energies (Ea) for the permeability of acetic acid decreased with decreasing phospholipid chain length and correlated with the sensitivity of chain ordering to temperature, [symbol: see text] sigma/[symbol: see text](1/T), as chain length was varied. Pm values decreased abruptly at temperatures below the main phase transition temperatures in pure dipalmitoylphosphatidylcholine and dimyristoylphosphatidylcholine bilayers (30-60-fold) and below the pretransition in dipalmitoylphosphatidylcholine bilayers (8-fold), and the linear relationship between in f and sigma established for liquid-crystalline bilayers was no longer followed. However, in both gel and liquid-crystalline phases in f was found to exhibit an inverse correlation with free surface area (in f = -0.31 - 29.1/af, where af is the average free area (in square angstroms) per lipid molecule). Thus, the lipid bilayer permeability of acetic acid can be predicted from the relevant chain-packing properties in the bilayer (free surface area), regardless of whether chain ordering is varied by changes in temperature, lipid chain length, cholesterol concentration, or bilayer phase structure, provided that temperature effects on permeant dehydration and diffusion and the chain-length effects on bilayer barrier thickness are properly taken into account. PMID:8994607

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents.

PubMed

Hezaveh, Samira; Samanta, Susruta; Milano, Giuseppe; Roccatano, Danilo

2012-03-28

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.

Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents

NASA Astrophysics Data System (ADS)

Hezaveh, Samira; Samanta, Susruta; Milano, Giuseppe; Roccatano, Danilo

2012-03-01

In this paper, the conformation and dynamics properties of polyethylene oxide (PEO) and polypropylene oxide (PPO) polymer chains at 298 K have been studied in the melt and at infinite dilution condition in water, methanol, chloroform, carbon tetrachloride, and n-heptane using molecular dynamics simulations. The calculated density of PEO melt with chain lengths of n = 2, 3, 4, 5 and, for PPO, n = 7 are in good agreement with the available experimental data. The conformational properties of PEO and PPO show an increasing gauche preference for the O-C-C-O dihedral in the following order water>methanol>chloroform>carbon tetrachloride = n-heptane. On the contrary, the preference for trans conformation has a maximum in carbon tetrachloride and n-heptane followed in the order by chloroform, methanol, and water. The PEO conformational preferences are in qualitative agreement with results of NMR studies. PEO chains formed different types of hydrogen bonds with polar solvent molecules. In particular, the occurrence of bifurcated hydrogen bonding in chloroform was also observed. Radii of gyration of PEO chains of length larger than n = 9 monomers showed a good agreement with light scattering data in water and in methanol. For the shorter chains the observed deviations are probably due to the enhanced hydrophobic effects caused by the terminal methyl groups. For PEO the fitting of end-to-end distance distributions with the semi-flexible chain model at 298 K provided persistence lengths of 0.375 and 0.387 nm in water and methanol, respectively. Finally, the radius of gyration of Pluronic P85 turned out to be 2.25 ± 0.4 nm at 293 K in water in agreement with experimental data.

Synthesis and surface activities of a novel di-hydroxyl-sulfate-betaine-type zwitterionic gemini surfactants

NASA Astrophysics Data System (ADS)

Geng, Xiang F.; Hu, Xing Q.; Xia, Ji J.; Jia, Xue C.

2013-04-01

A series of novel di-hydroxyl-sulfate-betaine-type zwitterionic gemini surfactants of 1,2-bis[N-ethyl-N-(2-hydroxyl-3-sulfopropyl)-alkylammonium] alkyl betaines (DBAs-n, where s and n represent the spacer length of 2, 4 and 6 and the hydrocarbon chain length of 8, 12, 14, 16 and 18, respectively) were synthesized by reacting alkylamine with sodium 3-chloro-2-hydroxypropanesulfonate (the alternative sulphonated agent), followed by the reactions with а,ω-dibromoalkyl and then ethyl bromide. Their adsorption and aggregation properties were investigated by means of equilibrium surface tension, dynamic light-scattering (DLS) and transmission electron microscopy (TEM). DBAs-n gemini surfactants showed excellent surface activities and packed tightly at the interface. For example, the minimum CMC value for DBAs-n series was of the order of 10-5 M and the surface tension of water can be decreased as low as 22.2 mN/m. It was also found that the aggregates of DBAs-n solutions were significantly dependent on their hydrocarbon chain lengths. The aggregates changed from vesicles to entangled fiber-like micelles as the chain length increased from dodecyl to tetradecyl.

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

Pham, Grace H.; Rana, Ambar S. J. B.; Korkmaz, E. Nihal

Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we comparemore » the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.« less

Distribution of dopant ions around poly(3,4-ethylenedioxythiophene) chains: a theoretical study.

PubMed

Casanovas, Jordi; Zanuy, David; Alemán, Carlos

2017-04-12

The effect of counterions and multiple polymer chains on the properties and structure of poly(3,4-ethylenedioxythiophene) (PEDOT) doped with ClO 4 - has been examined using density functional theory (DFT) calculations with periodic boundary conditions (PBCs). Calculations on a one-dimensional periodic model with four explicit polymer repeat units and two ClO 4 - molecules indicate that the latter are separated as much as possible, with the salt structure and band gap obtained from such ClO 4 - distribution being in excellent agreement with those determined experimentally. On the other hand, DFT calculations on periodic models that include two chains indicate that neighboring PEDOT chains are shifted along the molecular axis by a half of the repeat unit length, with dopant ions intercalated between the polymer molecules acting as cement. In order to support these structural features, classical molecular dynamics (MD) simulations have been performed on a multiphasic system consisting of 69 explicit PEDOT chains anchored onto a steel surface, explicit ClO 4 - anions embedded in the polymer matrix, and an acetonitrile phase layer onto the polymer matrix. Analyses of the radial distribution functions indicate that the all-anti conformation, the relative disposition of adjacent PEDOT chains and the distribution of ClO 4 - dopant ions are fully consistent with periodic DFT predictions. The agreement between two such different methodologies allows reinforcing the microscopic understanding of the PEDOT film structure.

Some structural features of the teichuronic acid of Bacillus licheniformis N.C.T.C. 6346 cell walls

PubMed Central

Hughes, R. C.; Thurman, P. F.

1970-01-01

A teichuronic acid, containing glucuronic acid and N-acetylgalactosamine, was purified from acid extracts of Bacillus licheniformis 6346 cell walls as described by Janczura, Perkins & Rogers (1961). After reduction of the carboxyl function of glucuronic acid residues in the polysaccharide the reduced polymer contains equimolar amounts of N-acetylgalactosamine and glucose. Methylation of the reduced polysaccharide by the Hakamori (1964) technique showed the glucose residues to be substituted on C-4. A disaccharide, 3-O-glucuronosylgalactosamine, was isolated from partial acid hydrolysates of teichuronic acid. After N-acetylation the disaccharide produces chromogen readily on heating at pH7, in agreement with C-3 substitution of the reducing N-acetylamino sugar. Teichuronic acid also produces chromogen under the same conditions, with concurrent elimination of a modified polysaccharide from C-3 of reducing terminal N-acetylgalactosamine residues of the teichuronic acid chains. The number-average chain lengths of several preparations of teichuronic acid were estimated from the amounts of chromogen produced in comparison with the N-acetylated disaccharide. The values obtained are in good agreement with the weight-average molecular weight determined by ultracentrifugal analysis. The reducing terminals of teichuronic acid are shown to be exclusively N-acetylgalactosamine by reduction with sodium boro[3H]hydride. The number-average chain lengths of the teichuronic acid preparations were estimated by the extent of in corporation of tritium and are in agreement with values obtained by the other methods. PMID:5419741

Large-amplitude nonlinear normal modes of the discrete sine lattices.

PubMed

Smirnov, Valeri V; Manevitch, Leonid I

2017-02-01

We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of π). Although this model has numerous applications in different fields of physics, it was studied earlier in the infinite limit only. The discrete chain with a finite length can be considered as a well analytical analog of the coarse-grain models of flexible polymers in the molecular dynamics simulations. The developed approach allows to find the dispersion relations for arbitrary amplitudes of the nonlinear normal modes. We emphasize that the long-wavelength approximation, which is described by well-known sine-Gordon equation, leads to an inadequate zone structure for the amplitudes of about π/2 even if the chain is long enough. An extremely complex zone structure at the large amplitudes corresponds to multiple resonances between nonlinear normal modes even with strongly different wave numbers. Due to the complexity of the dispersion relations the modes with shorter wavelengths may have smaller frequencies. The stability of the nonlinear normal modes under condition of the resonant interaction are discussed. It is shown that this interaction of the modes in the vicinity of the long wavelength edge of the spectrum leads to the localization of the oscillations. The thresholds of instability and localization are determined explicitly. The numerical simulation of the dynamics of a finite-length chain is in a good agreement with obtained analytical predictions.

Partition thermodynamics of ionic surfactants between phosphatidylcholine vesicle and water phases

NASA Astrophysics Data System (ADS)

Chu, Shin-Chi; Hung, Chia-Hui; Wang, Shun-Cheng; Tsao, Heng-Kwong

2003-08-01

The partition of ionic surfactants (sodium alkyl sulfate and alkyl trimethyl ammonium bromide) between phosphatidylcholine vesicles and aqueous phase is investigated by simple conductometry under different temperatures. The experimental results can be well represented by the proposed regular solution theory and the thermodynamic parameters satisfy the thermodynamic consistency. The deviation from ideal partition is manifested through the effective interaction energy between lipid and surfactant wb, which is O(kT) large. It is found that wb rises as the alkyl chain is decreased for a specified head group. This is attributed to significant mismatch of chain lengths between surfactant and lipid molecules. The partition coefficient K declines with increasing temperature. The energy barrier from bilayer to aqueous phase, Δμ/kT∝ln K, is in the range of 16-26 kJ/mol. As the alkyl chain length is decreased for a given head group, Δμ is lowered by 1.3-1.5 kJ/mol per methylene group. Two independent analyses are employed to confirm this result. Using the thermodynamic parameters determined from experiments, the internal energy, entropy, and free energy of the partition process can be derived. Partition is essentially driven by the internal energy gain. The solubilizing ability, which is represented by the maximum surfactant-lipid ratio in the bilayer, Reb also decreases in accord with the K parameter. It is because the change in temperature influences the surfactant incorporation into the bilayer more than the formation of micelles.

Single polysaccharide assembly protein that integrates polymerization, termination, and chain-length quality control

PubMed Central

Williams, Danielle M.; Ovchinnikova, Olga G.; Koizumi, Akihiko; Mainprize, Iain L.; Kimber, Matthew S.; Lowary, Todd L.

2017-01-01

Lipopolysaccharides (LPS) are essential outer membrane glycolipids in most gram-negative bacteria. Biosynthesis of the O-antigenic polysaccharide (OPS) component of LPS follows one of three widely distributed strategies, and similar processes are used to assemble other bacterial surface glycoconjugates. This study focuses on the ATP-binding cassette (ABC) transporter-dependent pathway, where glycans are completed on undecaprenyl diphosphate carriers at the cytosol:membrane interface, before export by the ABC transporter. We describe Raoultella terrigena WbbB, a prototype for a family of proteins that, remarkably, integrates several key activities in polysaccharide biosynthesis into a single polypeptide. WbbB contains three glycosyltransferase (GT) modules. Each of the GT102 and GT103 modules characterized here represents a previously unrecognized GT family. They form a polymerase, generating a polysaccharide of [4)-α-Rhap-(1→3)-β-GlcpNAc-(1→] repeat units. The polymer chain is terminated by a β-linked Kdo (3-deoxy-d-manno-oct-2-ulosonic acid) residue added by a third GT module belonging to the recently discovered GT99 family. The polymerase GT modules are separated from the GT99 chain terminator by a coiled-coil structure that forms a molecular ruler to determine product length. Different GT modules in the polymerase domains of other family members produce diversified OPS structures. These findings offer insight into glycan assembly mechanisms and the generation of antigenic diversity as well as potential tools for glycoengineering. PMID:28137848

Leptin and leptin receptor gene polymorphisms are correlated with production performance in the Arctic fox.

PubMed

Zhang, M; Bai, X J

2015-05-25

The polymerase chain reaction-single-strand conformation polymorphism technique was employed to measure mononucleotide diversity in the coding region of the leptin and leptin receptor genes in the Arctic fox. The relationships between specific genetic mutations and reproductive performance in Arctic foxes were determined to im-prove breeding strategies. We found that a leptin gene polymorphism was significantly associated with body weight (P < 0.01), abdominal circumference (P < 0.01), and fur length (P < 0.01). Furthermore, a polymorphism in the leptin receptor gene was associated with carcass weight and guard hair length (P < 0.01). Leptin and leptin receptor gene combinatorial genotypes were significantly associated with abdominal circumference, fur length (P < 0.01), and body weight (P < 0.05). The leptin gene is thus a key gene affecting body weight, abdominal circumference, and fur length in Arctic foxes, whereas variations in the leptin receptor mainly affect carcass weight and guard hair. The marker loci identified in this study can be used to assist in the selection of Arctic foxes for breeding to raise the production performance of this species.

Oleogustus: The Unique Taste of Fat.

PubMed

Running, Cordelia A; Craig, Bruce A; Mattes, Richard D

2015-09-01

Considerable mechanistic data indicate there may be a sixth basic taste: fat. However, evidence demonstrating that the sensation of nonesterified fatty acids (NEFA, the proposed stimuli for "fat taste") differs qualitatively from other tastes is lacking. Using perceptual mapping, we demonstrate that medium and long-chain NEFA have a taste sensation that is distinct from other basic tastes (sweet, sour, salty, and bitter). Although some overlap was observed between these NEFA and umami taste, this overlap is likely due to unfamiliarity with umami sensations rather than true similarity. Shorter chain fatty acids stimulate a sensation similar to sour, but as chain length increases this sensation changes. Fat taste oral signaling, and the different signals caused by different alkyl chain lengths, may hold implications for food product development, clinical practice, and public health policy. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Linear and nonlinear susceptibilities from diffusion quantum Monte Carlo: application to periodic hydrogen chains.

PubMed

Umari, P; Marzari, Nicola

2009-09-07

We calculate the linear and nonlinear susceptibilities of periodic longitudinal chains of hydrogen dimers with different bond-length alternations using a diffusion quantum Monte Carlo approach. These quantities are derived from the changes in electronic polarization as a function of applied finite electric field--an approach we recently introduced and made possible by the use of a Berry-phase, many-body electric-enthalpy functional. Calculated susceptibilities and hypersusceptibilities are found to be in excellent agreement with the best estimates available from quantum chemistry--usually extrapolations to the infinite-chain limit of calculations for chains of finite length. It is found that while exchange effects dominate the proper description of the susceptibilities, second hypersusceptibilities are greatly affected by electronic correlations. We also assess how different approximations to the nodal surface of the many-body wave function affect the accuracy of the calculated susceptibilities.

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

Alexeev, A. V.; Maltseva, D. V.; Ivanov, V. A., E-mail: ivanov@polly.phys.msu.ru

We study force-extension curves of a single semiflexible chain consisting of several rigid rods connected by flexible spacers. The atomic force microscopy and laser optical or magnetic tweezers apparatus stretching these rod-coil macromolecules are discussed. In addition, the stretching by external isotropic force is analyzed. The main attention is focused on computer simulation and analytical results. We demonstrate that the force-extension curves for rod-coil chains composed of two or three rods of equal length differ not only quantitatively but also qualitatively in different probe methods. These curves have an anomalous shape for a chain of two rods. End-to-end distributions ofmore » rod-coil chains are calculated by Monte Carlo method and compared with analytical equations. The influence of the spacer’s length on the force-extension curves in different probe methods is analyzed. The results can be useful for interpreting experiments on the stretching of rod-coil block-copolymers.« less

Self-Assembly of Narrowly Dispersed Brush Diblock Copolymers with Domain Spacing more than 100 nm

NASA Astrophysics Data System (ADS)

Gu, Weiyin; Sveinbjornsson, Benjamin; Hong, Sung Woo; Grubbs, Robert; Russell, Thomas

2012-02-01

Self-assembled structures of high molecular weight (MW), narrow molecular weight distribution brush block copolymers containing polylactic acid (PLA) and polystyrene (PS) side chains with similar MWs were studied in both the melt and thin films. The polynorbornene-backbone-based brush diblock copolymers containing approximately equal volume fractions of each block self-assembled into highly ordered lamellae with domain spacing over 100 nm, as revealed by SAXS, GISAXS and AFM. The domain size increased approximately linearly with backbone length, which indicated an extended conformation of the backbone in the ordered state. The length of side chains also played a significant role in terms of controlling the domain size. As the degree of polymerization (DP) increased, the symmetric brush diblock copolymers with longer side chains tended to form larger lamellar microdomains in comparison to those that have the same DP but shorter side chains.

Self-Assembly of Alkylammonium Chains on Montmorillonite: Effect of Interlayer Cations, CEC, and Chain Length

NASA Astrophysics Data System (ADS)

Chen, Hua; Li, Yingjun; Zhou, Yuanlin; Wang, Shanqiang; Zheng, Jian; He, Jiacai

2017-12-01

Recently, polymeric materials have been filled with synthetic or natural inorganic compounds in order to improve their properties. Especially, polymer clay nanocomposites have attracted both academic and industrial attention. Currently, the structure and physical phenomena of organoclays at molecular level are difficultly explained by existing experimental techniques. In this work, molecular dynamics (MD) simulation was executed using the CLAYFF and CHARMM force fields to evaluate the structural properties of organoclay such as basal spacing, interlayer density, energy and the arrangement of alkyl chains in the interlayer spacing. Our results are in good agreement with available experimental or other simulation data. The effects of interlayer cations (Na+, K+, Ca2+), the cation exchange capacity, and the alkyl chain length on the basal spacing and the structural properties are estimated. These simulations are expected to presage the microstructure of organo-montmorillonite and lead relevant engineering applications.

The Effect of Causal Chain Length on Counterfactual Conditional Reasoning

ERIC Educational Resources Information Center

Beck, Sarah R.; Riggs, Kevin J.; Gorniak, Sarah L.

2010-01-01

We investigated German and Nichols' finding that 3-year-olds could answer counterfactual conditional questions about short causal chains of events, but not long. In four experiments (N = 192), we compared 3- and 4-year-olds' performance on short and long causal chain questions, manipulating whether the child could draw on general knowledge to…

Enhancing Electrophoretic Display Lifetime: Thiol-Polybutadiene Evaporation Barrier Property Response to Network Microstructure

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

Cook, Caitlyn Christian

An evaporation barrier is required to enhance the lifetime of electrophoretic deposition (EPD) displays. As EPD functions on the basis of reversible deposition and resuspension of colloids suspended in a solvent, evaporation of the solvent ultimately leads to device failure. Incorporation of a thiol-polybutadiene elastomer into EPD displays enabled display lifetime surpassing six months in counting and catalyzed rigid display transition into a flexible package. Final flexible display transition to mass production compels an electronic-ink approach to encapsulate display suspension within an elastomer shell. Final thiol-polybutadiene photosensitive resin network microstructure was idealized to be dense, homogeneous, and expose an elasticmore » response to deformation. Research at hand details an approach to understanding microstructural change within display elastomers. Polybutadiene-based resin properties are modified via polymer chain structure, with and without added aromatic urethane methacrylate difunctionality, and in measuring network response to variation in thiol and initiator concentration. Dynamic mechanical analysis results signify that cross-linked segments within a difunctionalized polybutadiene network were on average eight times more elastically active than that of linked segments within a non-functionalized polybutadiene network. Difunctionalized polybutadiene samples also showed a 2.5 times greater maximum elastic modulus than non-functionalized samples. Hybrid polymer composed of both polybutadiene chains encompassed TE-2000 stiffness and B-1000 elasticity for use in encapsulating display suspension. Later experiments measured kinetic and rheological response due to alteration in dithiol cross-linker chain length via real time Fourier transform infrared spectroscopy and real-time dynamic rheology. Distinct differences were discovered between dithiol resin systems, as maximum thiol conversion achieved in short and long chain length dithiols was 86% and 11%, respectively. Oscillatory real-time rheological experiments confirmed a more uniform network to better dissipate applied shear in short chain length dithiol systems, as long chain length dithiols relayed a steep internal stress build-up due to less cross-links and chain entanglements. Thorough understanding of network formation aids the production of a stronger and impermeable elastomeric barrier for preservation of EPD displays.« less

Vapor pressures of 1,3-dialkylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids with long alkyl chains

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

Rocha, Marisa A. A., E-mail: lbsantos@fc.up.pt, E-mail: marisa.alexandra.rocha@gmail.com; Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven; Coutinho, João A. P.

2014-10-07

This work presents the vapor pressure at several temperatures for the 1,3-dialkylimidazolium bis(trifluoromethylsulfonyl)imide series, [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (N = 14, 16, 18, and 20), measured by a Knudsen effusion method combined with a quartz crystal microbalance. The thermodynamic properties of vaporization of the ionic liquids under study are analysed together with the results obtained previously for the shorter alkyl chain length [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (N = 2, 4, 6, 8, 10, and 12), in order to evaluate the effect of the alkyl side chains of the cation and to get additional insights concerning the nanostructuration of ionic liquids.more » The symmetry effect is explored, based on the comparison with the asymmetric imidazolium based ionic liquids, [C{sub N-1}C{sub 1}im][NTf{sub 2}]. A trend shift on the thermodynamic properties of vaporization along the alkyl side chains of the extended symmetric ionic liquids, around [C{sub 6}C{sub 6}im][NTf{sub 2}], was detected. An intensification of the odd-even effect was observed starting from [C{sub 6}C{sub 6}im][NTf{sub 2}], with higher enthalpies and entropies of vaporization for the odd numbered ionic liquids, [C{sub 7}C{sub 7}im][NTf{sub 2}] and [C{sub 9}C{sub 9}im][NTf{sub 2}]. Similar, but less pronounced, odd-even effect was found for the symmetric ionic liquids with lower alkyl side chains length, [C{sub N/2}C{sub N/2}im][NTf{sub 2}] (with N = 4, 6, 8, 10, and 12). This effect is related with the predominant orientation of the terminal methyl group of the alkyl chain to the imidazolium ring and their influence in the cation-anion interaction. The same Critical Alkyl length at the hexyl, (C{sub 6}C{sub 1}and C{sub 6}C{sub 6}) was found for both asymmetric and symmetric series indicating that the nanostructuration of the ionic liquids is related with alkyl chain length.« less

Sequence determination of synthesized chondroitin sulfate dodecasaccharides.

PubMed

Shioiri, Tatsumasa; Tsuchimoto, Jun; Watanabe, Hideto; Sugiura, Nobuo

2016-06-01

Chondroitin sulfate (CS) is a linear acidic polysaccharide composed of repeating disaccharide units of glucuronic acid and N-acetyl-d-galactosamine. The polysaccharide is modified with sulfate groups at different positions by a variety of sulfotransferases. CS chains exhibit various biological and pathological functions by interacting with cytokines and growth factors and regulating their signal transduction. The fine structure of the CS chain defines its specific biological roles. However, structural analysis of CS has been restricted to disaccharide analysis, hampering the understanding of the structure-function relationship of CS chains. Here, we chemo-enzymatically synthesized CS dodecasaccharides having various sulfate modifications using a bioreactor system of bacterial chondroitin polymerase mutants and various CS sulfotransferases. We developed a sequencing method for CS chains using the CS dodecasaccharides. The method consists of (i) labeling a reducing end with 2-aminopyridine (PA), (ii) partial digestion of CS with testicular hyaluronidase, followed by separation of PA-conjugated oligosaccharides with different chain lengths, (iii) limited digestion of these oligosaccharides with chondroitin lyase AC II into disaccharides, followed by labeling with 2-aminobenzamide, (iv) CS disaccharide analysis using a dual-fluorescence HPLC system (reversed-phase ion-pair and ion-exchange chromatography), and (v) estimation of the composition by calculating individual disaccharide ratios. This CS chain sequencing allows characterization of CS-modifying enzymes and provides a useful tool toward understanding the structure-function relationship of CS chains. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mechanical heterogeneity in ionic liquids

NASA Astrophysics Data System (ADS)

Veldhorst, Arno A.; Ribeiro, Mauro C. C.

2018-05-01

Molecular dynamics (MD) simulations of five ionic liquids based on 1-alkyl-3-methylimidazolium cations, [CnC1im]+, have been performed in order to calculate high-frequency elastic moduli and to evaluate heterogeneity of local elastic moduli. The MD simulations of [CnC1im][NO3], n = 2, 4, 6, and 8, assessed the effect of domain segregation when the alkyl chain length increases, and [C8C1im][PF6] assessed the effect of strength of anion-cation interaction. Dispersion curves of excitation energies of longitudinal and transverse acoustic, LA and TA, modes were obtained from time correlation functions of mass currents at different wavevectors. High-frequency sound velocity of LA modes depends on the alkyl chain length, but sound velocity for TA modes does not. High-frequency bulk and shear moduli, K∞ and G∞, depend on the alkyl chain length because of a density effect. Both K∞ and G∞ are strongly dependent on the anion. The calculation of local bulk and shear moduli was accomplished by performing bulk and shear deformations of the systems cooled to 0 K. The simulations showed a clear connection between structural and elastic modulus heterogeneities. The development of nano-heterogeneous structure with increasing length of the alkyl chain in [CnC1im][NO3] implies lower values for local bulk and shear moduli in the non-polar domains. The mean value and the standard deviations of distributions of local elastic moduli decrease when [NO3]- is replaced by the less coordinating [PF6]- anion.

Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression

PubMed Central

Polka, Jessica K.

2014-01-01

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases chain length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus can be modulated by altering a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof. PMID:25289183

The distribution of genome shared identical by descent for a pair of full sibs by means of the continuous time Markov chain

NASA Astrophysics Data System (ADS)

Julie, Hongki; Pasaribu, Udjianna S.; Pancoro, Adi

2015-12-01

This paper will allow Markov Chain's application in genome shared identical by descent by two individual at full sibs model. The full sibs model was a continuous time Markov Chain with three state. In the full sibs model, we look for the cumulative distribution function of the number of sub segment which have 2 IBD haplotypes from a segment of the chromosome which the length is t Morgan and the cumulative distribution function of the number of sub segment which have at least 1 IBD haplotypes from a segment of the chromosome which the length is t Morgan. This cumulative distribution function will be developed by the moment generating function.

Aqueous solubilities, vapor pressures, and 1-octanol-water partition coefficients for C9-C14 linear alkylbenzenes

USGS Publications Warehouse

Sherblom, P.M.; Gschwend, P.M.; Eganhouse, R.P.

1992-01-01

Measurements and estimates of aqueous solubilities, 1-octanol-water partition coefficients (Kow), and vapor pressures were made for 29 linear alkylbenzenes having alkyl chain lengths of 9-14 carbons. The ranges of values observed were vapor pressures from 0.002 to 0.418 Pa, log Kow, from 6.83 to 9.95, and aqueous solubilities from 4 to 38 nmol??L-1. Measured values exhibited a relationship to both the alkyl chain length and the position of phenyl substitution on the alkyl chain. Measurement of the aqueous concentrations resulting from equilibration of a mixture of alkylbenzenes yielded higher than expected values, indicating cosolute or other interactive effects caused enhanced aqueous concentrations of these compounds. ?? 1992 American Chemical Society.

Driven, underdamped Frenkel-Kontorova model on a quasiperiodic substrate

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

Vanossi, A.; Ro''der, J.; Bishop, A. R.

2001-01-01

We consider the underdamped dynamics of a chain of atoms subject to a dc driving force and a quasiperiodic substrate potential. The system has three inherent length scales which we take to be mutually incommensurate. We find that when the length scales are related by the spiral mean (a cubic irrational) there exists a value of the interparticle interaction strength above which the static friction is zero. When the length scales are related by the golden mean (a quadratic irrational) the static friction is always nonzero. >From considerations based on the connection of this problem to standard map theory, wemore » postulate that zero static friction is generally possible for incommensurate ratios of the length scales involved. However, when the length scales are quadratic irrationals, or have some commensurability with each other, the static friction will be nonzero for all choices of interaction parameters. We also comment on the nature of the depinning mechanisms and the steady states achieved by the moving chain.« less

Synthesis, electronic structure, molecular packing/morphology evolution, and carrier mobilities of pure oligo-/poly(alkylthiophenes).

PubMed

Zhang, Lei; Colella, Nicholas S; Liu, Feng; Trahan, Stephan; Baral, Jayanta K; Winter, H Henning; Mannsfeld, Stefan C B; Briseno, Alejandro L

2013-01-16

Monodispersed conjugated oligothiophenes are receiving attention in fundamental and applied science due to their interesting optical, optoelectronic, and charge transport properties. These "low molecular weight" polymers serve as model structures for the corresponding polymer analogues, which are inherently polydispersed. Here we report the synthesis, electronic structure, molecular packing/morphology, and charge transport properties of monodispersed oligothiophenes with up to six didodecylquaterthiophene (DDQT) building block repeat units (i.e., 24 thiophene units). At the point where the effective conjugation length is reached, the electronic structure showed convergence behavior to the corresponding polymer, poly(3,3"-didodecyl-quaterthiophene) (PQT-12). X-ray crystal structure analysis of the dimer (DDQT-2) showed that terminal thiophenes exhibit syn-conformations, similar to the terminal syn-conformations observed in the trimer (DDQT-3). The dimer also exhibits a rare bending of the terminal alkyl side chains in order to prevent steric hindrance with neighboring hydrogens attached to core thiophenes. Grazing incidence X-ray scattering measurements revealed a morphology evolution from small molecule-like packing to polymer-like packing in thin films, with a morphology transition occurring near the effective conjugation length. Charge transport measurements showed a mobility increase with decreasing chain length. We correlated the molecular packing and morphology to charge transport and determined that carrier mobilities are most sensitive to crystallinity and crystal grain misorientation. This indicates that molecular weight is not a decisive factor for improved carrier mobility in the low molecular weight region, but rather the degree in crystallinity and in-plane crystal orientation. These results represent a fundamental advancement in understanding the relationship between conjugation length and carrier mobilities in oligothiophene semiconductors.

Molecular, genetic, and topological characterization of O-antigen chain length regulation in Shigella flexneri.

PubMed

Morona, R; van den Bosch, L; Manning, P A

1995-02-01

The rfb region of Shigella flexneri encodes the proteins required to synthesize the O-antigen component of its cell surface lipopolysaccharides (LPS). We have previously reported that a region adjacent to rfb was involved in regulating the length distribution of the O-antigen polysaccharide chains (D. F. Macpherson et al., Mol. Microbiol. 5:1491-1499, 1991). The gene responsible has been identified in Escherichia coli O75 (called rol [R. A. Batchelor et al., J. Bacteriol. 173:5699-5704, 1991]) and in E. coli O111 and Salmonella enterica serovar typhimurium strain LT2 (called cld [D. A. Bastin et al., Mol. Microbiol. 5:2223-2231, 1991]). Through a combination of subcloning, deletion, and transposon insertion analysis, we have identified a gene adjacent to the S. flexneri rfb region which encodes a protein of 36 kDa responsible for the length distribution of O-antigen chains in LPS as seen on silver-stained sodium dodecyl sulfate-polyacrylamide gels. DNA sequence analysis identified an open reading frame (ORF) corresponding to the rol gene. The corresponding protein was almost identical in sequence to the Rol protein of E. coli O75 and was highly homologous to the functionally identical Cld proteins of E. coli O111 and S. enterica serovar typhimurium LT2. These proteins, together with ORF o349 adjacent to rfe, had almost identical hydropathy plots which predict membrane-spanning segments at the amino- and carboxy-terminal ends and a hydrophilic central region. We isolated a number of TnphoA insertions which inactivated the rol gene, and the fusion end points were determined. The PhoA+ Rol::PhoA fusion proteins had PhoA fused within the large hydrophilic central domain of Rol. These proteins were located in the whole-membrane fraction, and extraction with Triton X-100 indicated a cytoplasmic membrane location. This finding was supported by sucrose density gradient fractionation of the whole-cell membranes and of E. coli maxicells expressing L-[35S]methionine-labelled Rol protein. Hence, we interpret these data to indicate that the Rol protein is anchored into the cytoplasmic membrane via its amino- and carboxy-terminal ends but that the majority of the protein is located in the periplasmic space. To confirm that rol is responsible for the effects on O-antigen chain length observed with the cloned rfb genes in E. coli K-12, it was mutated in S. flexneri by insertion of a kanamycin resistance cartridge. The resulting strains produced LPS with O antigens of nonmodal chain length, thereby confirming the function of the rol gene product. We propose a model for the function of Rol protein in which it acts as a type of molecular chaperone to facilitate the interaction of the O-antigen ligase (RfaL) with the O-antigen polymerase (Rfc) and polymerized, acyl carrier lipid-linked, O-antigen chains. Analysis of the DNA sequence of the region identified a number of ORFs corresponding to the well-known gnd and hisIE genes. The rol gene was located immediately downstream of two ORFs with sequence similarity to the gene encoding UDPglucose dehydrogenase (HasB) of Streptococcus pyogenes. The ORFs arise because of a deletion or frameshift mutation within the gene we have termed udg (for UDPglucose dehydrogenase).

Isolation and characterization of full-length putative alcohol dehydrogenase genes from polygonum minus

NASA Astrophysics Data System (ADS)

Hamid, Nur Athirah Abd; Ismail, Ismanizan

2013-11-01

Polygonum minus, locally named as Kesum is an aromatic herb which is high in secondary metabolite content. Alcohol dehydrogenase is an important enzyme that catalyzes the reversible oxidation of alcohol and aldehyde with the presence of NAD(P)(H) as co-factor. The main focus of this research is to identify the gene of ADH. The total RNA was extracted from leaves of P. minus which was treated with 150 μM Jasmonic acid. Full-length cDNA sequence of ADH was isolated via rapid amplification cDNA end (RACE). Subsequently, in silico analysis was conducted on the full-length cDNA sequence and PCR was done on genomic DNA to determine the exon and intron organization. Two sequences of ADH, designated as PmADH1 and PmADH2 were successfully isolated. Both sequences have ORF of 801 bp which encode 266 aa residues. Nucleotide sequence comparison of PmADH1 and PmADH2 indicated that both sequences are highly similar at the ORF region but divergent in the 3' untranslated regions (UTR). The amino acid is differ at the 107 residue; PmADH1 contains Gly (G) residue while PmADH2 contains Cys (C) residue. The intron-exon organization pattern of both sequences are also same, with 3 introns and 4 exons. Based on in silico analysis, both sequences contain "classical" short chain alcohol dehydrogenases/reductases ((c) SDRs) conserved domain. The results suggest that both sequences are the members of short chain alcohol dehydrogenase family.

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

DOE PAGES

Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; ...

2016-02-04

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

Covalent bond force profile and cleavage in a single polymer chain

NASA Astrophysics Data System (ADS)

Garnier, Lionel; Gauthier-Manuel, Bernard; van der Vegte, Eric W.; Snijders, Jaap; Hadziioannou, Georges

2000-08-01

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.