End-growth/evaporation living polymerization kinetics revisited

NASA Astrophysics Data System (ADS)

Semenov, A. N.; Nyrkova, I. A.

2011-03-01

End-growth/evaporation kinetics in living polymer systems with "association-ready" free unimers (no initiator) is considered theoretically. The study is focused on the systems with long chains (typical aggregation number N ≫ 1) at long times. A closed system of continuous equations is derived and is applied to study the kinetics of the chain length distribution (CLD) following a jump of a parameter (T-jump) inducing a change of the equilibrium mean chain length from N0 to N. The continuous approach is asymptotically exact for t ≫ t1, where t1 is the dimer dissociation time. It yields a number of essentially new analytical results concerning the CLD kinetics in some representative regimes. In particular, we obtained the asymptotically exact CLD response (for N ≫ 1) to a weak T-jump (ɛ = N0/N - 1 ≪ 1). For arbitrary T-jumps we found that the longest relaxation time tmax = 1/γ is always quadratic in N (γ is the relaxation rate of the slowest normal mode). More precisely tmax ∝4N2 for N0 < 2N and tmax ∝NN0/(1 - N/N0) for N0 > 2N. The mean chain length Nn is shown to change significantly during the intermediate slow relaxation stage t1 ≪ t ≪ tmax . We predict that N_n(t)-N_n(0)∝ √{t} in the intermediate regime for weak (or moderate) T-jumps. For a deep T-quench inducing strong increase of the equilibrium Nn (N ≫ N0 ≫ 1), the mean chain length follows a similar law, N_n(t)∝ √{t}, while an opposite T-jump (inducing chain shortening, N0 ≫ N ≫ 1) leads to a power-law decrease of Nn: Nn(t)∝t-1/3. It is also shown that a living polymer system gets strongly polydisperse in the latter regime, the maximum polydispersity index r = Nw/Nn being r* ≈ 0.77N0/N ≫ 1. The concentration of free unimers relaxes mainly during the fast process with the characteristic time tf ˜ t1N0/N2. A nonexponential CLD dominated by short chains develops as a result of the fast stage in the case of N0 = 1 and N ≫ 1. The obtained analytical results are supported, in part, by comparison with numerical results found both previously and in the present paper.

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

Wujcik, Kevin H.; Wang, Dunyang Rita; Pascal, Tod A.

Lithium sulfur (Li-S) batteries are well known for their high theoretical specific capacities, but are plagued with scientific obstacles that make practical implementation of the technology impossible. The success of Li-S batteries will likely necessitate the use of thick sulfur cathodes that enable high specific energy densities. However, little is known about the fundamental reaction mechanisms and chemical processes that take place in thick cathodes, as most research has focused on studying thinner cathodes that enable high performance. In this study, in situ X-ray absorption spectroscopy at the sulfur K-edge is used to examine the back of a 115 μmmore » thick Li-S cathode during discharge. Our results show that in such systems, where electrochemical reactions between sulfur and lithium are likely to proceed preferentially toward the front of the cathode, lithium polysulfide dianions formed in this region diffuse to the back of the cathode during discharge. We show that high conversion of elemental sulfur is achieved by chemical reactions between elemental sulfur and polysulfide dianions of intermediate chain length (Li 2S x, 4 ≤ x ≤ 6). Our work suggests that controlling the formation and diffusion of intermediate chain length polysulfide dianions is crucial for insuring full utilization of thick sulfur cathodes.« less

Expected distributions of root-mean-square positional deviations in proteins.

PubMed

Pitera, Jed W

2014-06-19

The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as "intermediates" or well-defined stable states.

Electrochemical mineralization of perfluorocarboxylic acids (PFCAs) by ce-doped modified porous nanocrystalline PbO2 film electrode.

PubMed

Niu, Junfeng; Lin, Hui; Xu, Jiale; Wu, Hao; Li, Yangyang

2012-09-18

The Ce-doped modified porous nanocrystalline PbO(2) film electrode prepared by electrodeposition technology was used for electrochemical mineralization of environmentally persistent perfluorinated carboxylic acids (PFCAs) (~C(4)-C(8)), i.e., perfluorobutanoic acid (PFBA), perfluopentanoic acid (PFPeA), perfluorohexanoic acid (PFHxA), perfluoheptanoic acid (PFHpA), and perfluorooctanoic acid (PFOA) in aqueous solution (100 mL of 100 mg L(-1)). The degradation of PFCAs follows pseudo-first-order kinetics, and the values of the relative rate constant (k) depend upon chain length k(PFHpA) (4.1 × 10(-2) min(-1); corresponding half-life 16.8 min) ≈ 1.1k(PFOA) ≈ 2.5k(PFHxA)≈ 6.9k(PFPeA) ≈ 9.7k(PFBA). The carbon mineralization indices [i.e., 1 - (TOC(insolution)/TOC(inPFCA,degraded))] were 0.49, 0.70, 0.84, 0.91, and 0.95 for PFBA, PFPeA, PFHxA, PFHpA, and PFOA, respectively, after 90 min electrolysis. The major mineralization product, F(-), as well as low amount of intermediate PFCAs with shortened chain lengths were detected in aqueous solution. By observing the intermediates and tracking the concentration change, a possible pathway of electrochemical mineralization is proposed as follows: Kolbe decarboxylation reaction occurs first at the anode to form the perfluoroalkyl radical, followed by reaction with hydroxyl radicals to form the perfluoroalkyl alcohol which then undergoes intramolecular rearrangement to form the perfluoroalkyl fluoride. After this, the perfluoroalkyl fluoride reforms perfluorinated carboxylic with shorter chain length than its origin by hydrolysis. This electrochemical technique could be employed to treat PFCAs (~C(4)-C(8)) in contaminated wastewater.

Beyond the Bend: Exploring the Conformational Landscape of Decyl, Undecyl, and Dodecylbenzene

NASA Astrophysics Data System (ADS)

Hewett, Daniel M.; Zwier, Timothy S.

2017-06-01

Alkylbenzenes are important components in the combustion process: they make up 20-30% of petroleum fuels and are intermediates on the pathway to soot formation. Understanding their conformational preferences is a vital step in understanding the processes by which fuels begin their journey from small, simple hydrocarbons into the large, graphitic masses of soot. Previous work done in our group, in collaboration with the Sibert group, found that the smallest alkylbenzene which folds its chain back over the ring is octylbenzene. The population of the lone folded structure in octylbenzene is low; however, theory predicts a rapid stabilization of the folded conformations relative to more extended structures as the chain length is increased, suggesting a likely shift in population towards folded structures. This talk will focus on our exploration of this possibility by discussing the UV excitation and single conformation IR spectra of decyl, undecyl, and dodecylbenzene, where increasing chain length allows for multiple stable folded configurations.

Analysis of the intermediate size proteoglycans from the developing chick limb buds.

PubMed

Vasan, N

1982-08-01

Limb-bud proteoglycans are heterogeneous molecules which vary in their chemical and physical properties with development. This report describes proteoglycan intermediates (PG-I) that predominate in stage-34 limbs, and compares them with proteoglycan aggregates (PG-A) in stage-38 limbs. We analysed proteoglycans and their components extracted with guanidinium chloride by subjecting them to density gradient centrifugation, molecular sieve chromatography, electrophoretic separation, and selective enzymatic degradation. PG-I and PG-A have similar chondroitin sulphate composition, amino sugars, chondroitin sulphate side-chain length, glycoprotein link factors, and hyaluronic acid binding capacity, and both cross react with antisera prepared against cartilage-specific chick sternal proteoglycans. However, PG-I has lower molecular weight, lower buoyant density, and fewer chondroitin sulphate side chains on the protein core. The PG-I in the developing limb can be considered a mixture of smaller aggregates and cartilage-specific large monomers in which the former predominate.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions.

PubMed

Abraham, Alex; Chatterji, Apratim

2018-04-21

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

NASA Astrophysics Data System (ADS)

Abraham, Alex; Chatterji, Apratim

2018-04-01

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Systems metabolic engineering design: Fatty acid production as an emerging case study

PubMed Central

Tee, Ting Wei; Chowdhury, Anupam; Maranas, Costas D; Shanks, Jacqueline V

2014-01-01

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities. PMID:24481660

Systems metabolic engineering design: fatty acid production as an emerging case study.

PubMed

Tee, Ting Wei; Chowdhury, Anupam; Maranas, Costas D; Shanks, Jacqueline V

2014-05-01

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities. © 2014 Wiley Periodicals, Inc.

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.

Temporal variation in pelagic food chain length in response to environmental change

PubMed Central

Ruiz-Cooley, Rocio I.; Gerrodette, Tim; Fiedler, Paul C.; Chivers, Susan J.; Danil, Kerri; Ballance, Lisa T.

2017-01-01

Climate variability alters nitrogen cycling, primary productivity, and dissolved oxygen concentration in marine ecosystems. We examined the role of this variability (as measured by six variables) on food chain length (FCL) in the California Current (CC) by reconstructing a time series of amino acid–specific δ15N values derived from common dolphins, an apex pelagic predator, and using two FCL proxies. Strong declines in FCL were observed after the 1997–1999 El Niño Southern Oscillation (ENSO) event. Bayesian models revealed longer FCLs under intermediate conditions for surface temperature, chlorophyll concentration, multivariate ENSO index, and total plankton volume but not for hypoxic depth and nitrate concentration. Our results challenge the prevalent paradigm that suggested long-term stability in the food web structure in the CC and, instead, reveal that pelagic food webs respond strongly to disturbances associated with ENSO events, local oceanography, and ongoing changes in climate. PMID:29057322

WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia

PubMed Central

Patel-King, Ramila S.; Gilberti, Renée M.; Hom, Erik F. Y.; King, Stephen M.

2013-01-01

Retrograde intraflagellar transport (IFT) is required for assembly of cilia. We identify a Chlamydomonas flagellar protein (flagellar-associated protein 163 [FAP163]) as being closely related to the D1bIC(FAP133) intermediate chain (IC) of the dynein that powers this movement. Biochemical analysis revealed that FAP163 is present in the flagellar matrix and is actively trafficked by IFT. Furthermore, FAP163 copurified with D1bIC(FAP133) and the LC8 dynein light chain, indicating that it is an integral component of the retrograde IFT dynein. To assess the functional role of FAP163, we generated an RNA interference knockdown of the orthologous protein (WD60) in planaria. The Smed-wd60(RNAi) animals had a severe ciliary assembly defect that dramatically compromised whole-organism motility. Most cilia were present as short stubs that had accumulated large quantities of IFT particle–like material between the doublet microtubules and the membrane. The few remaining approximately full-length cilia had a chaotic beat with a frequency reduced from 24 to ∼10 Hz. Thus WD60/FAP163 is a dynein IC that is absolutely required for retrograde IFT and ciliary assembly. PMID:23864713

Small angle neutron scattering from 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids ([Cnmim][PF6], n=4, 6, and 8)

NASA Astrophysics Data System (ADS)

Hardacre, Christopher; Holbrey, John D.; Mullan, Claire L.; Youngs, Tristan G. A.; Bowron, Daniel T.

2010-08-01

The presence of local anisotropy in the bulk, isotropic, and ionic liquid phases—leading to local mesoscopic inhomogeneity—with nanoscale segregation and expanding nonpolar domains on increasing the length of the cation alkyl-substituents has been proposed on the basis of molecular dynamics (MD) simulations. However, there has been little conclusive experimental evidence for the existence of intermediate mesoscopic structure between the first/second shell correlations shown by neutron scattering on short chain length based materials and the mesophase structure of the long chain length ionic liquid crystals. Herein, small angle neutron scattering measurements have been performed on selectively H/D-isotopically substituted 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids with butyl, hexyl, and octyl substituents. The data show the unambiguous existence of a diffraction peak in the low-Q region for all three liquids which moves to longer distances (lower Q), sharpens, and increases in intensity with increasing length of the alkyl substituent. It is notable, however, that this peak occurs at lower values of Q (longer length scale) than predicted in any of the previously published MD simulations of ionic liquids, and that the magnitude of the scattering from this peak is comparable with that from the remainder of the amorphous ionic liquid. This strongly suggests that the peak arises from the second coordination shells of the ions along the vector of alkyl-chain substituents as a consequence of increasing the anisotropy of the cation, and that there is little or no long-range correlated nanostructure in these ionic liquids.

Longitudinal relaxation of initially straight flexible and stiff polymers

NASA Astrophysics Data System (ADS)

Dimitrakopoulos, Panagiotis; Dissanayake, Inuka

2004-11-01

The present talk considers the relaxation of a single flexible or stiff polymer chain from an initial straight configuration in a viscous solvent. This problem commonly arises when strong flows are turned off in both industrial and biological applications. The problem is also motivated by recent experiments with single biopolymer molecules relaxing after being fully extended by applied forces as well as by the recent development of micro-devices involving stretched tethered biopolymers. Our results are applicable to a wide array of synthetic polymers such as polyacrylamides, Kevlar and polyesters as well as biopolymers such as DNA, actin filaments, microtubules and MTV. In this talk we discuss the mechanism of the polymer relaxation as was revealed through Brownian Dynamics simulations covering a broad range of time scales and chain stiffness. After the short-time free diffusion, the chain's longitudinal reduction at early intermediate times is shown to constitute a universal behavior for any chain stiffness caused by a quasi-steady relaxation of tensions associated with the deforming action of the Brownian forces. Stiff chains are shown to exhibit a late intermediate-time longitudinal reduction associated with a relaxation of tensions affected by the deforming Brownian and the restoring bending forces. The longitudinal and transverse relaxations are shown to obey different laws, i.e. the chain relaxation is anisotropic at all times. In the talk, we show how from the knowledge of the relaxation mechanism, we can predict and explain the polymer properties including the polymer stress and the solution birefringence. In addition, a generalized stress-optic law is derived valid for any time and chain stiffness. All polymer properties which depend on the polymer length are shown to exhibit two intermediate-time behaviors with the early one to constitute a universal behavior for any chain stiffness. This work was supported in part by the Minta Martin Research Fund. The computations were performed on multiprocessor computers provided by the National Center for Supercomputing Applications (NCSA) in Illinois (grant DMR000003), and by an Academic Equipment Grant from Sun Microsystems Inc.

Intermediates of peroxisomal beta-oxidation. A study of the fatty acyl-CoA esters which accumulate during peroxisomal beta-oxidation of [U-14C]hexadecanoate.

PubMed Central

Bartlett, K; Hovik, R; Eaton, S; Watmough, N J; Osmundsen, H

1990-01-01

1. 14C-labelled fatty acyl-CoA esters resulting from beta-oxidation of [U-14C]hexadecanoate by peroxisomal fractions isolated from rats treated with clofibrate showed the presence of the full range of saturated intermediates down to acetyl-CoA. 2. The pattern of intermediates generated was fairly constant. At low concentrations of [U-14C]hexadecanoate (50 microM), decanoyl-CoA was present in lowest amounts. At higher concentrations of [U-14C]hexadecanoate (greater than 100 microM), all intermediates of chain length shorter than 12 carbon atoms (except acetyl-CoA) were present at similar low concentrations; the process of beta-oxidation now resembling chain-shortening of hexadecanoate by two cycles of beta-oxidation. 3. In the absence of an NAD(+)-regenerating system [pyruvate and lactate dehydrogenase (EC 1.1.1.28)] 2-enoyl- and 3-hydroxyacyl-CoA esters were generated, suggesting that re-oxidation of NADH is essential for optimal rates of peroxisomal beta-oxidation in vitro. 4. At high concentrations of [U-14C]hexadecanoate (greater than 100 microM), 3-oxohexadecanoyl-CoA was produced, suggesting that thiolase (acetyl-CoA acetyltransferase; EC 2.3.1.9) can become rate-limiting for peroxisomal beta-oxidation. Images Fig. 2. Fig. 3. Fig. 4. PMID:2396977

Theoretical and computational studies of excitons in conjugated polymers

NASA Astrophysics Data System (ADS)

Barford, William; Bursill, Robert J.; Smith, Richard W.

2002-09-01

We present a theoretical and computational analysis of excitons in conjugated polymers. We use a tight-binding model of π-conjugated electrons, with 1/r interactions for large r. In both the weak-coupling limit (defined by W>>U) and the strong-coupling limit (defined by W<

In Situ X-ray Absorption Spectroscopy Studies of Discharge Reactions in a Thick Cathode of a Lithium Sulfur Battery

DOE PAGES

Wujcik, Kevin H.; Wang, Dunyang Rita; Pascal, Tod A.; ...

2016-12-01

Lithium sulfur (Li-S) batteries are well known for their high theoretical specific capacities, but are plagued with scientific obstacles that make practical implementation of the technology impossible. The success of Li-S batteries will likely necessitate the use of thick sulfur cathodes that enable high specific energy densities. However, little is known about the fundamental reaction mechanisms and chemical processes that take place in thick cathodes, as most research has focused on studying thinner cathodes that enable high performance. In this study, in situ X-ray absorption spectroscopy at the sulfur K-edge is used to examine the back of a 115 μmmore » thick Li-S cathode during discharge. Our results show that in such systems, where electrochemical reactions between sulfur and lithium are likely to proceed preferentially toward the front of the cathode, lithium polysulfide dianions formed in this region diffuse to the back of the cathode during discharge. We show that high conversion of elemental sulfur is achieved by chemical reactions between elemental sulfur and polysulfide dianions of intermediate chain length (Li 2S x, 4 ≤ x ≤ 6). Our work suggests that controlling the formation and diffusion of intermediate chain length polysulfide dianions is crucial for insuring full utilization of thick sulfur cathodes.« less

Detailed dimethylacetal and fatty acid composition of rumen content from lambs fed lucerne or concentrate supplemented with soybean oil.

PubMed

Alves, Susana P; Santos-Silva, José; Cabrita, Ana R J; Fonseca, António J M; Bessa, Rui J B

2013-01-01

Lipid metabolism in the rumen is responsible for the complex fatty acid profile of rumen outflow compared with the dietary fatty acid composition, contributing to the lipid profile of ruminant products. A method for the detailed dimethylacetal and fatty acid analysis of rumen contents was developed and applied to rumen content collected from lambs fed lucerne or concentrate based diets supplemented with soybean oil. The methodological approach developed consisted on a basic/acid direct transesterification followed by thin-layer chromatography to isolate fatty acid methyl esters from dimethylacetal, oxo- fatty acid and fatty acid dimethylesters. The dimethylacetal composition was quite similar to the fatty acid composition, presenting even-, odd- and branched-chain structures. Total and individual odd- and branched-chain dimethylacetals were mostly affected by basal diet. The presence of 18:1 dimethylacetals indicates that biohydrogenation intermediates might be incorporated in structural microbial lipids. Moreover, medium-chain fatty acid dimethylesters were identified for the first time in the rumen content despite their concentration being relatively low. The fatty acids containing 18 carbon-chain lengths comprise the majority of the fatty acids present in the rumen content, most of them being biohydrogenation intermediates of 18:2n-6 and 18:3n-3. Additionally, three oxo- fatty acids were identified in rumen samples, and 16-O-18:0 might be produced during biohydrogenation of the 18:3n-3.

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.

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

PubMed Central

Gray, Harry B.; Winkler, Jay R.

2015-01-01

Living organisms have adapted to atmospheric dioxygen by exploiting its oxidizing power while protecting themselves against toxic side effects. Reactive oxygen and nitrogen species formed during oxidative stress, as well as high-potential reactive intermediates formed during enzymatic catalysis, could rapidly and irreversibly damage polypeptides were protective mechanisms not available. Chains of redox-active tyrosine and tryptophan residues can transport potentially damaging oxidizing equivalents (holes) away from fragile active sites and toward protein surfaces where they can be scavenged by cellular reductants. Precise positioning of these chains is required to provide effective protection without inhibiting normal function. A search of the structural database reveals that about one third of all proteins contain Tyr/Trp chains composed of three or more residues. Although these chains are distributed among all enzyme classes, they appear with greatest frequency in the oxidoreductases and hydrolases. Consistent with a redox-protective role, approximately half of the dioxygen-using oxidoreductases have Tyr/Trp chain lengths ≥3 residues. Among the hydrolases, long Tyr/Trp chains appear almost exclusively in the glycoside hydrolases. These chains likely are important for substrate binding and positioning, but a secondary redox role also is a possibility. PMID:26195784

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.

Respiratory Syncytial Virus Genomic Load and Disease Severity Among Children Hospitalized With Bronchiolitis: Multicenter Cohort Studies in the United States and Finland

PubMed Central

Hasegawa, Kohei; Jartti, Tuomas; Mansbach, Jonathan M.; Laham, Federico R.; Jewell, Alan M.; Espinola, Janice A.; Piedra, Pedro A.; Camargo, Carlos A.

2015-01-01

Background. We investigated whether children with a higher respiratory syncytial virus (RSV) genomic load are at a higher risk of more-severe bronchiolitis. Methods. Two multicenter prospective cohort studies in the United States and Finland used the same protocol to enroll children aged <2 years hospitalized for bronchiolitis and collect nasopharyngeal aspirates. By using real-time polymerase chain reaction analysis, patients were classified into 3 genomic load status groups: low, intermediate, and high. Outcome measures were a length of hospital stay (LOS) of ≥3 days and intensive care use, defined as admission to the intensive care unit or use of mechanical ventilation. Results. Of 2615 enrolled children, 1764 (67%) had RSV bronchiolitis. Children with a low genomic load had a higher unadjusted risk of having a length of stay of ≥3 days (52%), compared with children with intermediate and those with high genomic loads (42% and 51%, respectively). In a multivariable model, the risk of having a length of stay of ≥3 days remained significantly higher in the groups with intermediate (odds ratio [OR], 1.43; 95% confidence interval [CI], 1.20–1.69) and high (OR, 1.58; 95% CI, 1.29–1.94) genomic loads. Similarly, children with a high genomic load had a higher risk of intensive care use (20%, compared with 15% and 16% in the groups with low and intermediate genomic loads, respectively). In a multivariable model, the risk remained significantly higher in the group with a high genomic load (OR, 1.43; 95% CI, 1.03–1.99). Conclusion. Children with a higher RSV genomic load had a higher risk for more-severe bronchiolitis. PMID:25425699

The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis.

PubMed

Marchetti, Piera M; Kelly, Van; Simpson, Joanna P; Ward, Mairi; Campopiano, Dominic J

2018-04-18

The marine bacterium Pseudoalteromonas tunicata produces the bipyrrole antibiotic tambjamine YP1. This natural product is built from common amino acid and fatty acid building blocks in a biosynthetic pathway that is encoded in the tam operon which contains 19 genes. The exact role that each of these Tam proteins plays in tambjamine biosynthesis is not known. Here, we provide evidence that TamA initiates the synthesis and controls the chain length of the essential tambjamine fatty amine tail. Sequence analysis suggests the unusual TamA is comprised of an N-terminal adenylation (ANL) domain fused to a C-terminal acyl carrier protein (ACP). Mass spectrometry analysis of recombinant TamA revealed the surprising presence of bound C11 and C12 acyl-adenylate intermediates. Acylation of the ACP domain was observed upon attachment of the phosphopantetheine (4'-PP) arm to the ACP. We also show that TamA can transfer fatty acids ranging in chain length from C6-C13 to an isolated ACP domain. Thus TamA bridges the gap between primary and secondary metabolism by linking fatty acid and pyrrole biosynthetic pathways.

Localization and elasticity in entangled polymer liquids as a mesoscopic glass transition

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth

2010-03-01

The reptation-tube model is widely viewed as the correct zeroth order model for entangled linear polymer dynamics under quiescent conditions. Its key ansatz is the existence of a mesoscopic dynamical length scale that prohibits transverse chain motion beyond a tube diameter of order 3-10 nm. However, the theory is phenomenological and lacks a microscopic foundation, and many fundamental questions remain unanswered. These include: (i) where does the confining tube field come from and can it be derived from statistical mechanics? (ii) what is the microscopic origin of the magnitude, and power law scaling with concentration and packing length, of the plateau shear modulus? (iii) is the tube diameter time-dependent? (iv) does the confinement field contribute to elasticity ? (v) do entanglement constraints have a finite strength? Building on our new force-level theories for the dynamical crossover and activated barrier hopping in glassy colloidal suspensions and polymer melts, a first principles self-consistent theory has been developed for entangled polymers. Its basic physical elements, and initial results that address the questions posed above, will be presented. The key idea is that beyond a critical degree of polymerization, the chain connectivity and excluded volume induced intermolecular correlation hole drives temporary localization on an intermediate length scale resulting in a mesoscopic ``ideal kinetic glass transition.'' Large scale isotropic motion is effectively quenched due to the emergence of chain length dependent entropic barriers. However, the barrier height is not infinite, resulting in softening of harmonic localization at large displacements, temporal increase of the confining length scale, and a finite strength of entanglement constraints which can be destroyed by applied stress.

Intermediate-filaments: from disordered building blocks to well-ordered cells

NASA Astrophysics Data System (ADS)

Kornreich, Micha; Malka-Gibor, Eti; Laser-Azogui, Adi; Doron, Ofer; Avinery, Ram; Herrmann, Harald; Beck, Roy

In the past decade it was found that ~50% of human proteins contain long disordered regions, which play significant functional roles. As these regions lack a defined 3D folded structure, their ensemble conformations can be studied using polymer physics statistical-mechanics arguments. We measure the structure and mechanical response of hydrogels composed of neuronal intermediate filaments proteins. In the nervous system, these proteins provide cells with their mechanical support and shape, via interactions of their long, highly charged and disordered protein chains. We employ synchrotron small-angle X-ray scattering and various microscopy techniques to investigate such hydrogels from the nano- to the macro-scale. In contrast to previous polymer physics theories and experiments, we find that shorter and less charged chains can promote network expansion. The results are explained by intricate interactions between specific domains on the interacting chains, and also suggest a novel structural justification for the changing protein compositions observed during neuronal development. We address the following questions: Can protein disorder have an important role in cellular architecture? Can structural disorder in the micro-scale induce orientational and translational order on the macro-scale? How do the physical properties of disordered protein regions, such as charge, length, and hydrophobicity, modulate the cellular super-structure?

Functionalized Congeners of P2Y1 Receptor Antagonists:

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

de Castro, Sonia; Maruoka, Hiroshi; Hong, Kunlun

2010-01-01

The P2Y{sub 1} receptor is a prothrombotic G protein-coupled receptor (GPCR) activated by ADP. Preference for the North (N) ring conformation of the ribose moiety of adenine nucleotide 3',5'-bisphosphate antagonists of the P2Y{sub 1} receptor was established by using a ring-constrained methanocarba (a bicyclo[3.1.0]hexane) ring as a ribose substitute. A series of covalently linkable N{sup 6}-methyl-(N)-methanocarba-2'-deoxyadenosine-3',5'-bisphosphates containing extended 2-alkynyl chains was designed, and binding affinity at the human (h) P2Y{sub 1} receptor determined. The chain of these functionalized congeners contained hydrophilic moieties, a reactive substituent, or biotin, linked via an amide. Variation of the chain length and position of anmore » intermediate amide group revealed high affinity of carboxylic congener 8 (K{sub i} 23 nM) and extended amine congener 15 (K{sub i} 132 nM), both having a 2-(1-pentynoyl) group. A biotin conjugate 18 containing an extended {epsilon}-aminocaproyl spacer chain exhibited higher affinity than a shorter biotinylated analogue. Alternatively, click coupling of terminal alkynes of homologous 2-dialkynyl nucleotide derivatives to alkyl azido groups produced triazole derivatives that bound to the P2Y{sub 1} receptor following deprotection of the bisphosphate groups. The preservation of receptor affinity of the functionalized congeners was consistent with new P2Y{sub 1} receptor modeling and ligand docking. Attempted P2Y{sub 1} antagonist conjugation to PAMAM dendrimer carriers by amide formation or palladium-catalyzed reaction between an alkyne on the dendrimer and a 2-iodopurine-derivatized nucleotide was unsuccessful. A dialkynyl intermediate containing the chain length favored in receptor binding was conjugated to an azide-derivatized dendrimer, and the conjugate inhibited ADP-promoted human platelet aggregation. This is the first example of attaching a strategically functionalized P2Y receptor antagonist to a PAMAM dendrimer to produce a multivalent conjugate exhibiting a desired biological effect, i.e., antithrombotic action.« less

Elucidation of the sex-pheromone biosynthesis producing 5,7-dodecadienes in Dendrolimus punctatus (Lepidoptera: Lasiocampidae) reveals Delta 11- and Delta 9-desaturases with unusual catalytic properties.

PubMed

Liénard, Marjorie A; Lassance, Jean-Marc; Wang, Hong-Lei; Zhao, Cheng-Hua; Piskur, Jure; Johansson, Tomas; Löfstedt, Christer

2010-06-01

Sex pheromones produced by female moths of the Lasiocampidae family include conjugated 5,7-dodecadiene components with various oxygenated terminal groups. Here we describe the molecular cloning, heterologous expression and functional characterization of desaturases associated with the biosynthesis of these unusual chemicals. By homology-based PCR screening we characterized five cDNAs from the female moth pheromone gland that were related to other moth desaturases, and investigated their role in the production of the (Z)-5-dodecenol and (Z5,E7)-dodecadienol, major pheromone constituents of the pine caterpillar moth, Dendrolimus punctatus. Functional expression of two desaturase cDNAs belonging to the Delta 11-subfamily, Dpu-Delta 11(1)-APSQ and Dpu-Delta 11(2)-LPAE, showed that they catalysed the formation of unsaturated fatty acyls (UFAs) that can be chain-shortened by beta-oxidation and subsequently reduced to the alcohol components. A first (Z)-11-desaturation step is performed by Dpu-Delta 11(2)-LPAE on stearic acid that leads to (Z)-11-octadecenoic acyl, which is subsequently chain shortened to the (Z)-5-dodecenoic acyl precursor. The Dpu-Delta 11(1)-APSQ desaturase had the unusual property of producing Delta 8 mono-UFA of various chain lengths, but not when transformed yeast were grown in presence of (Z)-9-hexadecenoic acyl, in which case the biosynthetic intermediate (Z9,E11)-hexadecadienoic UFA was produced. In addition to a typical Z9 activity, a third transcript, Dpu-Delta 9-KPSE produced E9 mono-UFAs of various chain lengths. When provided with the (Z)-7-tetradecenoic acyl, it formed the (Z7,E9)-tetradecadienoic UFA, another biosynthetic intermediate that can be chain-shortened to (Z5,E7)-dodecadienoic acyl. Both Dpu-Delta 11(1)-APSQ and Dpu-Delta 9-KPSE thus exhibited desaturase activities consistent with the biosynthesis of the dienoic precursor. The combined action of three desaturases in generating a dienoic sex-pheromone component emphasizes the diversity and complexity of chemical reactions that can be catalysed by pheromone biosynthetic fatty-acyl-CoA desaturases in moths. (c) 2010 Elsevier Ltd. All rights reserved.

Dechlorination of short chain chlorinated paraffins by nanoscale zero-valent iron.

PubMed

Zhang, Zhi-Yong; Lu, Mang; Zhang, Zhong-Zhi; Xiao, Meng; Zhang, Min

2012-12-01

In this study, nanoscale zero-valent iron (NZVI) particles were synthesized and used for the reductive dehalogenation of short chain chlorinated paraffins (SCCPs) in the laboratory. The results show that the dechlorination rate of chlorinated n-decane (CP(10)) by NZVI increased with decreased solution pH. Increasing the loading of NZVI enhanced the dechlorination rate of CP(10). With an increase in temperature, the degradation rate increased. The reduction of CP(10) by NZVI was accelerated with increasing the concentration of humic acid up to 15 mg/L but then was inhibited. The dechlorination of CP(10) within the initial 18 h followed pseudo-first order rate model. The formation of intermediate products indicates a stepwise dechlorination pathway of SCCPs by NZVI. The carbon chain length and chlorination degree of SCCPs have a polynominal impact on dechlorination reactions. Copyright © 2012 Elsevier B.V. All rights reserved.

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow with hydrodynamic interaction

NASA Astrophysics Data System (ADS)

Hoda, Nazish; Kumar, Satish

2007-12-01

The adsorption of single polyelectrolyte molecules in shear flow is studied using Brownian dynamics simulations with hydrodynamic interaction (HI). Simulations are performed with bead-rod and bead-spring chains, and electrostatic interactions are incorporated through a screened Coulombic potential with excluded volume accounted for by the repulsive part of a Lennard-Jones potential. A correction to the Rotne-Prager-Yamakawa tensor is derived that accounts for the presence of a planar wall. The simulations show that migration away from an uncharged wall, which is due to bead-wall HI, is enhanced by increases in the strength of flow and intrachain electrostatic repulsion, consistent with kinetic theory predictions. When the wall and polyelectrolyte are oppositely charged, chain behavior depends on the strength of electrostatic screening. For strong screening, chains get depleted from a region close to the wall and the thickness of this depletion layer scales as N1/3Wi2/3 at high Wi, where N is the chain length and Wi is the Weissenberg number. At intermediate screening, bead-wall electrostatic attraction competes with bead-wall HI, and it is found that there is a critical Weissenberg number for desorption which scales as N-1/2κ-3(lB∣σq∣)3/2, where κ is the inverse screening length, lB is the Bjerrum length, σ is the surface charge density, and q is the bead charge. When the screening is weak, adsorbed chains are observed to align in the vorticity direction at low shear rates due to the effects of repulsive intramolecular interactions. At higher shear rates, the chains align in the flow direction. The simulation method and results of this work are expected to be useful for a number of applications in biophysics and materials science in which polyelectrolyte adsorption plays a key role.

Unit and internal chain profiles of maca amylopectin.

PubMed

Zhang, Ling; Li, Guantian; Yao, Weirong; Zhu, Fan

2018-03-01

Unit chain length distributions of amylopectin and its φ, β-limit dextrins, which reflect amylopectin internal structure from three maca starches, were determined by high-performance anion-exchange chromatography with pulsed amperometric detection after debranching, and the samples were compared with maize starch. The amylopectins exhibited average chain lengths ranging from 16.72 to 17.16, with ranges of total internal chain length, external chain length, and internal chain length of the maca amylopectins at 12.49 to 13.68, 11.24 to 11.89, and 4.27 to 4.48. The average chain length, external chain length, internal chain length, and total internal chain length were comparable in three maca amylopectins. Amylopectins of the three maca genotypes studied here presented no significant differences in their unit chain length profiles, but did show significant differences in their internal chain profiles. Additional genetic variations between different maca genotypes need to be studied to provide unit- and internal chain profiles of maca amylopectin. Copyright © 2017. Published by Elsevier Ltd.

Detailed Dimethylacetal and Fatty Acid Composition of Rumen Content from Lambs Fed Lucerne or Concentrate Supplemented with Soybean Oil

PubMed Central

Alves, Susana P.; Santos-Silva, José; Cabrita, Ana R. J.; Fonseca, António J. M.; Bessa, Rui J. B.

2013-01-01

Lipid metabolism in the rumen is responsible for the complex fatty acid profile of rumen outflow compared with the dietary fatty acid composition, contributing to the lipid profile of ruminant products. A method for the detailed dimethylacetal and fatty acid analysis of rumen contents was developed and applied to rumen content collected from lambs fed lucerne or concentrate based diets supplemented with soybean oil. The methodological approach developed consisted on a basic/acid direct transesterification followed by thin-layer chromatography to isolate fatty acid methyl esters from dimethylacetal, oxo- fatty acid and fatty acid dimethylesters. The dimethylacetal composition was quite similar to the fatty acid composition, presenting even-, odd- and branched-chain structures. Total and individual odd- and branched-chain dimethylacetals were mostly affected by basal diet. The presence of 18∶1 dimethylacetals indicates that biohydrogenation intermediates might be incorporated in structural microbial lipids. Moreover, medium-chain fatty acid dimethylesters were identified for the first time in the rumen content despite their concentration being relatively low. The fatty acids containing 18 carbon-chain lengths comprise the majority of the fatty acids present in the rumen content, most of them being biohydrogenation intermediates of 18∶2n−6 and 18∶3n−3. Additionally, three oxo- fatty acids were identified in rumen samples, and 16-O-18∶0 might be produced during biohydrogenation of the 18∶3n−3. PMID:23484024

Synthesis of Polyformate Esters of Vegetable Oils: Milkweed, Pennycress, and Soy.

PubMed

Harry-O'kuru, Rogers E; Biresaw, Girma; Tisserat, Brent; Evangelista, Roque

2016-01-01

In a previous study of the characteristics of acyl derivatives of polyhydroxy milkweed oil (PHMWO), it was observed that the densities and viscosities of the respective derivatives decreased with increased chain length of the substituent acyl group. Thus from the polyhydroxy starting material, attenuation in viscosity of the derivatives relative to PHMWO was found in the order: PHMWO ≫ PAcMWE ≫ PBuMWE ≫ PPMWE (2332 : 1733 : 926.2 : 489.4 cSt, resp., at 40°C), where PAcMWE, PBuMWE, and PPMWE were the polyacetyl, polybutyroyl, and polypentanoyl ester derivatives, respectively. In an analogous manner, the densities also decreased as the chain length increased although not as precipitously compared to the viscosity drop. By inference, derivatives of vegetable oils with short chain length substituents on the triglyceride would be attractive in lubricant applications in view of their higher densities and possibly higher viscosity indices. Pursuant to this, we have explored the syntheses of formyl esters of three vegetable oils in order to examine the optimal density, viscosity, and related physical characteristics in relation to their suitability as lubricant candidates. In the absence of ready availability of formic anhydride, we opted to employ the epoxidized vegetable oils as substrates for formyl ester generation using glacial formic acid. The epoxy ring-opening process was smooth but was apparently followed by a simultaneous condensation reaction of the putative α-hydroxy formyl intermediate to yield vicinal diformyl esters from the oxirane. All three polyformyl esters milkweed, soy, and pennycress derivatives exhibited low coefficient of friction and a correspondingly much lower wear scar in the 4-ball antiwear test compared to the longer chain acyl analogues earlier studied.

Synthesis of Polyformate Esters of Vegetable Oils: Milkweed, Pennycress, and Soy

PubMed Central

Harry-O'kuru, Rogers E.; Biresaw, Girma; Tisserat, Brent; Evangelista, Roque

2016-01-01

In a previous study of the characteristics of acyl derivatives of polyhydroxy milkweed oil (PHMWO), it was observed that the densities and viscosities of the respective derivatives decreased with increased chain length of the substituent acyl group. Thus from the polyhydroxy starting material, attenuation in viscosity of the derivatives relative to PHMWO was found in the order: PHMWO ≫ PAcMWE ≫ PBuMWE ≫ PPMWE (2332 : 1733 : 926.2 : 489.4 cSt, resp., at 40°C), where PAcMWE, PBuMWE, and PPMWE were the polyacetyl, polybutyroyl, and polypentanoyl ester derivatives, respectively. In an analogous manner, the densities also decreased as the chain length increased although not as precipitously compared to the viscosity drop. By inference, derivatives of vegetable oils with short chain length substituents on the triglyceride would be attractive in lubricant applications in view of their higher densities and possibly higher viscosity indices. Pursuant to this, we have explored the syntheses of formyl esters of three vegetable oils in order to examine the optimal density, viscosity, and related physical characteristics in relation to their suitability as lubricant candidates. In the absence of ready availability of formic anhydride, we opted to employ the epoxidized vegetable oils as substrates for formyl ester generation using glacial formic acid. The epoxy ring-opening process was smooth but was apparently followed by a simultaneous condensation reaction of the putative α-hydroxy formyl intermediate to yield vicinal diformyl esters from the oxirane. All three polyformyl esters milkweed, soy, and pennycress derivatives exhibited low coefficient of friction and a correspondingly much lower wear scar in the 4-ball antiwear test compared to the longer chain acyl analogues earlier studied. PMID:26955488

High flexibility of DNA on short length scales probed by atomic force microscopy.

PubMed

Wiggins, Paul A; van der Heijden, Thijn; Moreno-Herrero, Fernando; Spakowitz, Andrew; Phillips, Rob; Widom, Jonathan; Dekker, Cees; Nelson, Philip C

2006-11-01

The mechanics of DNA bending on intermediate length scales (5-100 nm) plays a key role in many cellular processes, and is also important in the fabrication of artificial DNA structures, but previous experimental studies of DNA mechanics have focused on longer length scales than these. We use high-resolution atomic force microscopy on individual DNA molecules to obtain a direct measurement of the bending energy function appropriate for scales down to 5 nm. Our measurements imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical elasticity models such as the worm-like chain (WLC) model. For example, we found that on short length scales, spontaneous large-angle bends are many times more prevalent than predicted by the WLC model. We test our data and model with an interlocking set of consistency checks. Our analysis also shows how our model is compatible with previous experiments, which have sometimes been viewed as confirming the WLC.

Isomer effects on polyimide properties

NASA Technical Reports Server (NTRS)

Stump, B. L.

1975-01-01

The effect of structure variation on the solubility and glass-transition temperature of polyimide polymers is investigated. The addition of alkyl substituents to an aromatic ring in the polymer molecule, the reduction in the number of imide rings per average polymer chain-length, and a variation in the symmetry of the polymer molecule are studied. The synthesis of key intermediates for the preparation of the monomers required in this investigation is reported along with progress made in the synthesis of polyimide-precursor amines that contain functional groups to allow for post-cure cross-linking.

An experimental study of search in global social networks.

PubMed

Dodds, Peter Sheridan; Muhamad, Roby; Watts, Duncan J

2003-08-08

We report on a global social-search experiment in which more than 60,000 e-mail users attempted to reach one of 18 target persons in 13 countries by forwarding messages to acquaintances. We find that successful social search is conducted primarily through intermediate to weak strength ties, does not require highly connected "hubs" to succeed, and, in contrast to unsuccessful social search, disproportionately relies on professional relationships. By accounting for the attrition of message chains, we estimate that social searches can reach their targets in a median of five to seven steps, depending on the separation of source and target, although small variations in chain lengths and participation rates generate large differences in target reachability. We conclude that although global social networks are, in principle, searchable, actual success depends sensitively on individual incentives.

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

Isolated starches from yams (Dioscorea sp) grown at the Venezuelan Amazons: structure and functional properties.

PubMed

Pérez, Elevina; Rolland-Sabaté, Agnès; Dufour, Dominique; Guzmán, Romel; Tapia, María; Raymundez, Marìa; Ricci, Julien; Guilois, Sophie; Pontoire, Bruno; Reynes, Max; Gibert, Olivier

2013-10-15

This work aimed to characterize the molecular structure and functional properties of starches isolated from wild Dioscorea yams grown at the Amazons, using conventional and up-to-date methodologies. Among the high purity starches isolated (≥99%), the chain lengths were similar, whereas variations in gelatinization profile were observed. Starches have shown varied-shaped granules with monomodal distribution, and B-type crystallinity. Variations in amylose contents found by three analyses were hypothesized being related to intermediate material. Linear chain lengths were similar, and their amylopectins showed a dense, spherical conformation and similar molecular characteristics. The average molar mass and the radius of gyration of the chromatograms of the yam amylopectin, M¯W and R¯G were ranging between 174×10(6) g mol(-1) and 237×10(6) g mol(-1), and 201 nm and 233 nm, respectively. The white yams starches were more sensible to enzymes than the other two. All starches have shown a wide range of functional and nutritional properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Partial deletion of beta9 loop in pancreatic lipase-related protein 2 reduces enzyme activity with a larger effect on long acyl chain substrates.

PubMed

Dridi, Kaouthar; Amara, Sawsan; Bezzine, Sofiane; Rodriguez, Jorge A; Carrière, Frédéric; Gaussier, Hélène

2013-07-01

Structural studies on pancreatic lipase have revealed a complex architecture of surface loops surrounding the enzyme active site and potentially involved in interactions with lipids. Two of them, the lid and beta loop, expose a large hydrophobic surface and are considered as acyl chain binding sites based on their interaction with an alkyl phosphonate inhibitor. While the role of the lid in substrate recognition and selectivity has been extensively studied, the implication of beta9 loop in acyl chain stabilization remained hypothetical. The characterization of an enzyme with a natural deletion of the lid, guinea pig pancreatic lipase-related protein 2 (GPLRP2), suggests however an essential contribution of the beta9 loop in the stabilization of the acyl enzyme intermediate formed during the lipolysis reaction. A GPLRP2 mutant with a seven-residue deletion of beta9 loop (GPLRP2-deltabeta9) was produced and its enzyme activity was measured using various substrates (triglycerides, monoglycerides, galactolipids, phospholipids, vinyl esters) with short, medium and long acyl chains. Whatever the substrate tested, GPLRP2-deltabeta9 activity is drastically reduced compared to that of wild-type GPLRP2 and this effect is more pronounced as the length of substrate acyl chain increases. Changes in relative substrate selectivity and stereoselectivity remained however weak. The deletion within beta9 loop has also a negative effect on the rate of enzyme inhibition by alkyl phosphonates. All these findings indicate that the reduced enzyme turnover observed with GPLRP2-deltabeta9 results from a weaker stabilization of the acyl enzyme intermediate due to a loss of hydrophobic interactions.

Alkyl Chain Length Dependent Structural and Orientational Transformations of Water at Alcohol-Water Interfaces and Its Relevance to Atmospheric Aerosols.

PubMed

Mondal, Jahur A; Namboodiri, V; Mathi, P; Singh, Ajay K

2017-04-06

Although the hydrophobic size of an amphiphile plays a key role in various chemical, biological, and atmospheric processes, its effect at macroscopic aqueous interfaces (e.g., air-water, oil-water, cell membrane-water, etc.), which are ubiquitous in nature, is not well understood. Here we report the hydrophobic alkyl chain length dependent structural and orientational transformations of water at alcohol (C n H 2n+1 OH, n = 1-12)-water interfaces using interface-selective heterodyne-detected vibrational sum frequency generation (HD-VSFG) and Raman multivariate curve resolution (Raman-MCR) spectroscopic techniques. The HD-VSFG results reveal that short-chain alcohols (C n H 2n+1 OH, n < 4, i.e., up to 1-propanol) do not affect the structure (H-bonding) and orientation of water at the air-water interface; the OH stretch band maximum appears at ∼3470 cm -1 , and the water H atoms are pointed toward the bulk water, that is, "H-down" oriented. In contrast, long-chain alcohols (C n H 2n+1 OH, n > 4, i.e., beyond 1-butanol) make the interfacial water more strongly H-bonded and reversely orientated; the OH stretch band maximum appears at ∼3200 cm -1 , and the H atoms are pointed away from the bulk water, that is, "H-up" oriented. Interestingly, for the alcohol of intermediate chain length (C n H 2n+1 OH, n = 4, i.e, 1-butanol), the interface is quite unstable even after hours of its formation and the time-averaged result is qualitatively similar to that of the long-chain alcohols, indicating a structural/orientational crossover of interfacial water at the 1-butanol-water interface. pH-dependent HD-VSFG measurements (with H 2 O as well as isotopically diluted water, HOD) suggest that the structural/orientational transformation of water at the long-chain alcohol-water interface is associated with the adsorption of OH - anion at the interface. Vibrational mapping of the water structure in the hydration shell of OH - anion (obtained by Raman-MCR spectroscopy of NaOH in HOD) clearly shows that the water becomes strongly H-bonded (OH stretch max. ≈ 3200 cm -1 ) while hydrating the OH - anion. Altogether, it is conceivable that alcohols of different hydrophobic chain lengths that are present in the troposphere will differently affect the interfacial electrostatics and associated chemical processes of aerosol droplets, which are critical for cloud formation, global radiation budget, and climate change.

Cellulose microfibril formation within a coarse grained molecular dynamics

NASA Astrophysics Data System (ADS)

Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration

2014-03-01

Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.

Disulfide oil hazard assessment using categorical analysis and a mode of action determination.

PubMed

Morgott, David; Lewis, Christopher; Bootman, James; Banton, Marcy

2014-01-01

Diethyl and diphenyl disulfides, naphtha sweetening (Chemical Abstracts Service [CAS] # 68955-96-4), are primarily composed of low-molecular-weight dialkyl disulfides extracted from C4 to C5 light hydrocarbon streams during the refining of crude oil. The substance, commonly known as disulfide oil (DSO), can be composed of up to 17 different disulfides and trisulfides with monoalkyl chain lengths no greater than C4. The disulfides in DSO constitute a homologous series of chemical constituents that are perfectly suited for a hazard evaluation using a read-across/worst-case approach. The DSO constituents exhibit a common mode of action that is operable at all trophic levels. The observed oxidative stress response is mediated by reactive oxygen species and free radical intermediates generated after disulfide bond cleavage and subsequent redox cycling of the resulting mercaptan. Evidence indicates that the lowest series member, dimethyl disulfide (DMDS), can operate as a worst-case surrogate for other members of the series, since it displays the highest toxicity. Increasing the alkyl chain length or degree of substitution has been shown to serially reduce disulfide toxicity through resonance stabilization of the radical intermediate or steric inhibition of the initial enzymatic step. The following case study examines the mode of action for dialkyl disulfide toxicity and documents the use of read-across information from DMDS to assess the hazards of DSO. The results indicate that DSO possesses high aquatic toxicity, moderate environmental persistence, low to moderate acute toxicity, high repeated dose toxicity, and a low potential for genotoxicity, carcinogenicity, and reproductive/developmental effects.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Intermediate temperature proton conductors for PEM fuel cells based on phosphonic acid as protogenic group: a progress report.

PubMed

Steininger, H; Schuster, M; Kreuer, K D; Kaltbeitzel, A; Bingöl, B; Meyer, W H; Schauff, S; Brunklaus, G; Maier, J; Spiess, H W

2007-04-21

The melting behaviour and transport properties of straight chain alkanes mono- and difunctionalized with phosphonic acid groups have been investigated as a function of their length. The increase of melting temperature and decrease of proton conductivity with increasing chain length is suggested to be the consequence of an increasing ordering of the alkane segments which constrains the free aggregation of the phosphonic acid groups. However, the proton mobility is reduced to a greater extent than the proton diffusion coefficient indicating an increasing cooperativity of proton transport with increasing length of the alkane segment. The results clearly indicate that the "spacer concept", which had been proven successful in the optimization of the proton conductivity of heterocycle based systems, fails in the case of phosphonic acid functionalized polymers. Instead, a very high concentration of phosphonic acid functional groups forming "bulky" hydrogen bonded aggregates is suggested to be essential for obtaining very high proton conductivity. Aggregation is also suggested to reduce condensation reactions generally observed in phosphonic acid containing systems. On the basis of this understanding, the proton conductivities of poly(vinyl phosphonic acid) and poly(meta-phenylene phosphonic acid) are discussed. Though both polymers exhibit a substantial concentration of phosphonic acid groups, aggregation seems to be constrained to such an extent that intrinsic proton conductivity is limited to values below sigma = 10(-3) S cm(-1) at T = 150 degrees C. The results suggest that different immobilization concepts have to be developed in order to minimize the conductivity reduction compared to the very high intrinsic proton conductivity of neat phosphonic acid under quasi dry conditions. In the presence of high water activities, however, (as usually present in PEM fuel cells) the very high ion exchange capacities (IEC) possible for phosphonic acid functionalized ionomers (IEC >10 meq g(-1)) may allow for high proton conductivities in the intermediate temperature range (T approximately 120 -160 degrees C).

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).

Regulatory light chain mutants linked to heart disease modify the cardiac myosin lever arm.

PubMed

Burghardt, Thomas P; Sikkink, Laura A

2013-02-19

Myosin is the chemomechanical energy transducer in striated heart muscle. The myosin cross-bridge applies impulsive force to actin while consuming ATP chemical energy to propel myosin thick filaments relative to actin thin filaments in the fiber. Transduction begins with ATP hydrolysis in the cross-bridge driving rotary movement of a lever arm converting torque into linear displacement. Myosin regulatory light chain (RLC) binds to the lever arm and modifies its ability to translate actin. Gene sequencing implicated several RLC mutations in heart disease, and three of them are investigated here using photoactivatable GFP-tagged RLC (RLC-PAGFP) exchanged into permeabilized papillary muscle fibers. A single-lever arm probe orientation is detected in the crowded environment of the muscle fiber by using RLC-PAGFP with dipole orientation deduced from the three-spatial dimension fluorescence emission pattern of the single molecule. Symmetry and selection rules locate dipoles in their half-sarcomere, identify those at the minimal free energy, and specify active dipole contraction intermediates. Experiments were performed in a microfluidic chamber designed for isometric contraction, total internal reflection fluorescence detection, and two-photon excitation second harmonic generation to evaluate sarcomere length. The RLC-PAGFP reports apparently discretized lever arm orientation intermediates in active isometric fibers that on average produce the stall force. Disease-linked mutants introduced into RLC move intermediate occupancy further down the free energy gradient, implying lever arms rotate more to reach stall force because mutant RLC increases lever arm shear strain. A lower free energy intermediate occupancy involves a lower energy conversion efficiency in the fiber relating a specific myosin function modification to the disease-implicated mutant.

The roles of productivity and ecosystem size in determining food chain length in tropical terrestrial ecosystems.

PubMed

Young, Hillary S; McCauley, Douglas J; Dunbar, Robert B; Hutson, Michael S; Ter-Kuile, Ana Miller; Dirzo, Rodolfo

2013-03-01

Many different drivers, including productivity, ecosystem size, and disturbance, have been considered to explain natural variation in the length of food chains. Much remains unknown about the role of these various drivers in determining food chain length, and particularly about the mechanisms by which they may operate in terrestrial ecosystems, which have quite different ecological constraints than aquatic environments, where most food chain length studies have been thus far conducted. In this study, we tested the relative importance of ecosystem size and productivity in influencing food chain length in a terrestrial setting. We determined that (1) there is no effect of ecosystem size or productive space on food chain length; (2) rather, food chain length increases strongly and linearly with productivity; and (3) the observed changes in food chain length are likely achieved through a combination of changes in predator size, predator behavior, and consumer diversity along gradients in productivity. These results lend new insight into the mechanisms by which productivity can drive changes in food chain length, point to potential for systematic differences in the drivers of food web structure between terrestrial and aquatic systems, and challenge us to consider how ecological context may control the drivers that shape food chain length.

Long-Range Self-Assembly via the Mutual Lorentz Force of Plasmon Radiation.

PubMed

Ji, Haojie; Trevino, Jacob; Tu, Raymond; Knapp, Ellen; McQuade, James; Yurkiv, Vitaliy; Mashayek, Farzad; Vuong, Luat T

2018-04-11

Long-range interactions often proceed as a sequence of hopping through intermediate, statistically favored events. Here, we demonstrate predictable mechanical dynamics of particles that arise from the Lorentz force between plasmons. Even if the radiation is weak, the nonconservative Lorentz force produces stable locations perpendicular to the plasmon oscillation; over time, distinct patterns emerge. Experimentally, linearly polarized light illumination leads to the formation of 80 nm diameter Au nanoparticle chains, perpendicularly aligned, with lengths that are orders of magnitude greater than their plasmon near-field interaction. There is a critical intensity threshold and optimal concentration for observing self-assembly.

Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains

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

Sliozberg, Yelena R.; TKC Global, Inc., Aberdeen Proving Ground, Maryland 21005; Kröger, Martin

Equilibrated systems of entangled polymer melts cannot be produced using direct brute force equilibration due to the slow reptation dynamics exhibited by high molecular weight chains. Instead, these dense systems are produced using computational techniques such as Monte Carlo-Molecular Dynamics hybrid algorithms, though the use of soft potentials has also shown promise mainly for coarse-grained polymeric systems. Through the use of soft-potentials, the melt can be equilibrated via molecular dynamics at intermediate and long length scales prior to switching to a Lennard-Jones potential. We will outline two different equilibration protocols, which use various degrees of information to produce the startingmore » configurations. In one protocol, we use only the equilibrium bond angle, bond length, and target density during the construction of the simulation cell, where the information is obtained from available experimental data and extracted from the force field without performing any prior simulation. In the second protocol, we moreover utilize the equilibrium radial distribution function and dihedral angle distribution. This information can be obtained from experimental data or from a simulation of short unentangled chains. Both methods can be used to prepare equilibrated and highly entangled systems, but the second protocol is much more computationally efficient. These systems can be strictly monodisperse or optionally polydisperse depending on the starting chain distribution. Our protocols, which utilize a soft-core harmonic potential, will be applied for the first time to equilibrate a million particle system of polyethylene chains consisting of 1000 united atoms at various temperatures. Calculations of structural and entanglement properties demonstrate that this method can be used as an alternative towards the generation of entangled equilibrium structures.« less

Catalytic strategy for carbon−carbon bond scission by the cytochrome P450 OleT

PubMed Central

Grant, Job L.; Mitchell, Megan E.; Makris, Thomas Michael

2016-01-01

OleT is a cytochrome P450 that catalyzes the hydrogen peroxide-dependent metabolism of Cn chain-length fatty acids to synthesize Cn-1 1-alkenes. The decarboxylation reaction provides a route for the production of drop-in hydrocarbon fuels from a renewable and abundant natural resource. This transformation is highly unusual for a P450, which typically uses an Fe4+−oxo intermediate known as compound I for the insertion of oxygen into organic substrates. OleT, previously shown to form compound I, catalyzes a different reaction. A large substrate kinetic isotope effect (≥8) for OleT compound I decay confirms that, like monooxygenation, alkene formation is initiated by substrate C−H bond abstraction. Rather than finalizing the reaction through rapid oxygen rebound, alkene synthesis proceeds through the formation of a reaction cycle intermediate with kinetics, optical properties, and reactivity indicative of an Fe4+−OH species, compound II. The direct observation of this intermediate, normally fleeting in hydroxylases, provides a rationale for the carbon−carbon scission reaction catalyzed by OleT. PMID:27555591

Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics.

PubMed

Jas, Gouri S; Hegefeld, Wendy A; Middaugh, C Russell; Johnson, Carey K; Kuczera, Krzysztof

2014-07-03

We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in accord with the "broken zipper" model of Scheraga. The monotonic increase in length with temperature may be explained by the zipper-like breaking of the hairpin hydrogen bonds and backbone contacts.

Aquatic toxicity and biodegradability of advanced cationic surfactant APA-22 compatible with the aquatic environment.

PubMed

Yamane, Masayuki; Toyo, Takamasa; Inoue, Katsuhisa; Sakai, Takaya; Kaneko, Youhei; Nishiyama, Naohiro

2008-01-01

Cationic surfactant is a chemical substance used in hair conditioner, fabric softener and other household products. By investigating the relationship between the aquatic toxicity and the chemical structures of two types of mono alkyl cationic surfactants, alkyl trimethylammonium salts and alkyl dimethylamine salts, we have found that the C22 alkyl chain length is effective to reduce the toxicity. Besides, we have recognized that the amidopropyl functional group contributes to the enhanced biodegradability by investigating the biodegradation trend of (alkylamidopropyl)dimethylamine salt (alkyl chain length: C18). Based on these findings, we have developed mono alkyl cationic surfactant called APA-22, N-[3-(dimethylamino)propyl]docosanamide salt. APA-22 is formed by the C22 alkyl chain, amidopropyl functional group and di-methyltertiary amine group. We evaluated the aerobic and anaerobic biodegradability of APA-22 by two standard methods (OECD Test Guideline 301B and ECETOC technical document No.28) and found that this substance was degraded rapidly in both conditions. The toxicity to algae, invertebrate and fish of this substance are evaluated by using OECD Test Guideline 201, 202 and 203, respectively. All acute toxicity values are >1 mg/L, which indicates that environmental toxicity of this substance is relatively less toxic to aquatic organism. In addition, we estimated the biodegradation pathway of APA-22 and observed the complete disappearance of APA-22 and its intermediates during the test periods. Based on the environmental data provided above, we concluded that APA22 is more compatible with the aquatic environment compared to other cationic surfactants with mono long alkyl chain.

Inhibition mechanism of P-glycoprotein mediated efflux by mPEG-PLA and influence of PLA chain length on P-glycoprotein inhibition activity.

PubMed

Li, Wenjing; Li, Xinru; Gao, Yajie; Zhou, Yanxia; Ma, Shujin; Zhao, Yong; Li, Jinwen; Liu, Yan; Wang, Xinglin; Yin, Dongdong

2014-01-06

The present study aimed to investigate the effect of monomethoxy poly(ethylene glycol)-block-poly(D,L-lactic acid) (mPEG-PLA) on the activity of P-glycoprotein (P-gp) in Caco-2 cells and further unravel the relationship between PLA chain length in mPEG-PLA and influence on P-gp efflux and the action mechanism. The transport results of rhodamine 123 (R123) across Caco-2 cell monolayers suggested that mPEG-PLA unimers were responsible for its P-gp inhibitory effect. Furthermore, transport studies of R123 revealed that the inhibitory potential of P-gp efflux by mPEG-PLA analogues was strongly correlated with their structural features and showed that the hydrophilic mPEG-PLA copolymers with an intermediate PLA chain length and 10.20 of hydrophilic-lipophilic balance were more effective at inhibiting P-gp efflux in Caco-2 cells. The fluorescence polarization measurement results ruled out the plasma membrane fluidization as a contributor for inhibition of P-gp by mPEG-PLA. Concurrently, mPEG-PLA inhibited neither basal P-gp ATPase (ATP is adenosine triphosphate) activity nor substrate stimulated P-gp ATPase activity, suggesting that mPEG-PLA seemed not to be a substrate of P-gp and a competitive inhibitor. No evident alteration in P-gp surface level was detected by flow cytometry upon exposure of the cells to mPEG-PLA. The depletion of intracellular ATP, which was likely to be a result of partial inhibition of cellular metabolism, was directly correlated with inhibitory potential for P-gp mediated efflux by mPEG-PLA analogues. Hence, intracellular ATP-depletion appeared to be possible explanation to the inhibition mechanism of P-gp by mPEG-PLA. Taken together, the establishment of a relationship between PLA chain length and impact on P-gp efflux activity and interpretation of action mechanism of mPEG-PLA on P-gp are of fundamental importance and will facilitate future development of mPEG-PLA in the drug delivery area.

Molecular marker and stable carbon isotope analyses of carbonaceous Ambassador uranium ores of Mulga Rock in Western Australia

NASA Astrophysics Data System (ADS)

Jaraula, C.; Schwark, L.; Moreau, X.; Grice, K.; Bagas, L.

2013-12-01

Mulga Rock is a multi-element deposit containing uranium hosted by Eocene peats and lignites deposited in inset valleys incised into Permian rocks of the Gunbarrel Basin and Precambrian rocks of the Yilgarn Craton and Albany-Fraser Orogen. Uranium readily adsorbs onto minerals or phytoclasts to form organo-uranyl complexes. This is important in pre-concentrating uranium in this relatively young ore deposit with rare uraninite [UO2] and coffinite [U(SiO4)1-x(OH)4x], more commonly amorphous and sub-micron uranium-bearing particulates. Organic geochemical and compound-specific stable carbon isotope analyses were conducted to identify possible associations of molecular markers with uranium accumulation and to recognize effect(s) of ionizing radiation on molecular markers. Samples were collected from the Ambassador deposit containing low (<200 ppm) to high (>2000 ppm) uranium concentrations. The bulk rock C/N ratios of 82 to 153, Rock-Eval pyrolysis yields of 316 to 577 mg hydrocarbon/g TOC (Hydrogen Index, HI) and 70 to 102 mg CO2/g TOC (Oxygen Index, OI) are consistent with a terrigenous and predominantly vascular plant OM source deposited in a complex shallow water system, ranging from lacustrine to deltaic, swampy wetland and even shallow lake settings as proposed by previous workers. Organic solvent extracts were separated into saturated hydrocarbon, aromatic hydrocarbon, ketone, and a combined free fatty acid and alcohol fraction. The molecular profiles appear to vary with uranium concentration. In samples with relatively low uranium concentrations, long-chain n-alkanes, alcohols and fatty acids derived from epicuticular plant waxes dominate. The n-alkane distributions (C27 to C31) reveal an odd/even preference (Carbon Preference Index, CPI=1.5) indicative of extant lipids. Average δ13C of -27 to -29 ‰ for long-chain n-alkanes is consistent with a predominant C3 plant source. Samples with relatively higher uranium concentrations contain mostly intermediate-length n-alkanes, ketones, alcohols, and fatty acids (C20 to C24) with no preferential distribution (CPI~1). Intermediate length n-alkanes have modest carbon isotope enrichment compared to long-chain n-alkanes. These shorter-chain hydrocarbons are interpreted to represent alteration products. The diversity and relative abundance of ketones in highly mineralised Mulga Rock peats and lignites are not consistent with aerobic and diagenetic degradation of terrigenous OM in oxic environments. Moreover, molecular changes cannot be associated with thermal breakdown due to the low maturity of the deposits. It is possible that the association of high uranium concentrations and potential radiolysis resulted in the oxidation of alcohol functional groups into aldehydes and ketones and breakdown of highly aliphatic macromolecules (i.e. spores, pollen, cuticles, and algal cysts). These phytoclasts are usually considered to be recalcitrant as they evolved to withstand chemical and physical degradation. Previous petrographic analyses show that spores, pollen and wood fragments are preferentially enriched in uranium. Their molecular compositions are feasible sources of short- to intermediate-length n-alkanes that dominate the mineralised peats and lignites.

Dynamic Scaling Theory of the Forced Translocation of a Semi-flexible Polymer Through a Nanopore

NASA Astrophysics Data System (ADS)

Lam, Pui-Man; Zhen, Yi

2015-10-01

We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the tensile force propagates through the backbone of the polymer, as suggested by Sakaue and recently applied to study a completely flexible polymer with self-avoidance, by Dubbledam et al. For a semi-flexible polymer with a persistence length P, its statistics is self-avoiding for a very long chain. As the local force increases, the blob size starts to decrease. At the blob size , where a is the size of a monomer, the statistics becomes that of an ideal chain. As the blob size further decreases to below the persistence length P, the statistics is that of a rigid rod. We argue that semi-flexible polymer in translocation should include the three regions: a self-avoiding region, an ideal chain region and a rigid rod region, under uneven tension propagation, instead of a uniform scaling picture as in the case of a completely flexible polymer. In various regimes under the effect of weak, intermediate and strong driving forces we derive equations from which we can calculate the translocation time of the polymer. The translocation exponent is given by , where is an effective exponent for the end-to-end distance of the semi-flexible polymer, having a value between 1/2 and 3/5, depending on the total contour length of the polymer. Our results are of relevance for forced translocation of biological polymers such as DNA through a nanopore.

Intermediate-range order in simple metal-phosphate glasses: The effect of metal cations on the phosphate anion distribution

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

Sales, B.C.; Boatner, L.A.; Ramey, J.O.

1997-06-01

The technique of high-performance liquid chromatography (HPLC) has been used to probe the phosphate anion distribution in a variety of metal phosphate glasses including glasses made with trivalent metal cations (Al, In, Ga, La). The composition of each glass was chosen so that the average phosphate chain length was between 2 and 4 PO{sub 4} tetrahedra. The widths of the resulting phosphate anion distributions were determined directly from an analysis of the HPLC chromatograms. Literature values for the free energy of formation of the crystalline metal-orthophosphate compounds with respect to P{sub 2}O{sub 5} and the metal oxide, were compared tomore » the chromatogram widths. It was found that the smaller the energy of formation, the wider the distribution of phosphate chains, and the greater the ease of glass formation.« less

The Light Intermediate Chain 2 Subpopulation of Dynein Regulates Mitotic Spindle Orientation.

PubMed

Mahale, Sagar; Kumar, Megha; Sharma, Amit; Babu, Aswini; Ranjan, Shashi; Sachidanandan, Chetana; Mylavarapu, Sivaram V S

2016-12-23

Cytoplasmic dynein 1 is a multi-protein intracellular motor essential for mediating several mitotic functions, including the establishment of proper spindle orientation. The functional relevance and mechanistic distinctions between two discrete dynein subpopulations distinguished only by Light Intermediate Chain (LIC) homologues, LIC1 and LIC2 is unknown during mitosis. Here, we identify LIC2-dynein as the major mediator of proper spindle orientation and uncover its underlying molecular mechanism. Cortically localized dynein, essential for maintaining correct spindle orientation, consists majorly of LIC2-dynein, which interacts with cortical 14-3-3 ε- ζ and Par3, conserved proteins required for orienting the spindle. LIC2-dynein is also responsible for the majority of dynein-mediated asymmetric poleward transport of NuMA, helping focus microtubule minus ends. In addition, LIC2-dynein dominates in equatorially aligning chromosomes at metaphase and in regulating mitotic spindle length. Key mitotic functions of LIC2 were remarkably conserved in and essential for early embryonic divisions and development in zebrafish. Thus LIC2-dynein exclusively engages with two major cortical pathways to govern spindle orientation. Overall, we identify a novel selectivity of molecular interactions between the two LICs in mitosis as the underlying basis for their uneven distribution of labour in ensuring proper spindle orientation.

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.

Engineering Escherichia coli for Conversion of Glucose to Medium-Chain ω-Hydroxy Fatty Acids and α,ω-Dicarboxylic Acids.

PubMed

Bowen, Christopher H; Bonin, Jeff; Kogler, Anna; Barba-Ostria, Carlos; Zhang, Fuzhong

2016-03-18

In search of sustainable approaches to plastics production, many efforts have been made to engineer microbial conversions of renewable feedstock to short-chain (C2-C8) bifunctional polymer precursors (e.g., succinic acid, cadaverine, 1,4-butanediol). Less attention has been given to medium-chain (C12-C14) monomers such as ω-hydroxy fatty acids (ω-OHFAs) and α,ω-dicarboxylic acids (α,ω-DCAs), which are precursors to high performance polyesters and polyamides. Here we engineer a complete microbial conversion of glucose to C12 and C14 ω-OHFAs and α,ω-DCAs, with precise control of product chain length. Using an expanded bioinformatics approach, we screen a wide range of enzymes across phyla to identify combinations that yield complete conversion of intermediates to product α,ω-DCAs. Finally, through optimization of culture conditions, we enhance production titer of C12 α,ω-DCA to nearly 600 mg/L. Our results indicate potential for this microbial factory to enable commercially relevant, renewable production of C12 α,ω-DCA-a valuable precursor to the high-performance plastic, nylon-6,12.

Universal scaling for the quantum Ising chain with a classical impurity

NASA Astrophysics Data System (ADS)

Apollaro, Tony J. G.; Francica, Gianluca; Giuliano, Domenico; Falcone, Giovanni; Palma, G. Massimo; Plastina, Francesco

2017-10-01

We study finite-size scaling for the magnetic observables of an impurity residing at the end point of an open quantum Ising chain with transverse magnetic field, realized by locally rescaling the field by a factor μ ≠1 . In the homogeneous chain limit at μ =1 , we find the expected finite-size scaling for the longitudinal impurity magnetization, with no specific scaling for the transverse magnetization. At variance, in the classical impurity limit μ =0 , we recover finite scaling for the longitudinal magnetization, while the transverse one basically does not scale. We provide both analytic approximate expressions for the magnetization and the susceptibility as well as numerical evidences for the scaling behavior. At intermediate values of μ , finite-size scaling is violated, and we provide a possible explanation of this result in terms of the appearance of a second, impurity-related length scale. Finally, by going along the standard quantum-to-classical mapping between statistical models, we derive the classical counterpart of the quantum Ising chain with an end-point impurity as a classical Ising model on a square lattice wrapped on a half-infinite cylinder, with the links along the first circle modified as a function of μ .

Internal friction and mode relaxation in a simple chain model.

PubMed

Fugmann, S; Sokolov, I M

2009-12-21

We consider the equilibrium relaxation properties of the end-to-end distance and of the principal components in a one-dimensional polymer chain model with nonlinear interaction between the beads. While for the single-well potentials these properties are similar to the ones of a Rouse chain, for the double-well interaction potentials, modeling internal friction, they differ vastly from the ones of the harmonic chain at intermediate times and intermediate temperatures. This minimal description within a one-dimensional model mimics the relaxation properties found in much more complex polymer systems. Thus, the relaxation time of the end-to-end distance may grow by orders of magnitude at intermediate temperatures. The principal components (whose directions are shown to coincide with the normal modes of the harmonic chain, whatever interaction potential is assumed) not only display larger relaxation times but also subdiffusive scaling.

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.

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

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

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.

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.

Constraints on food chain length arising from regional metacommunity dynamics

PubMed Central

Calcagno, Vincent; Massol, François; Mouquet, Nicolas; Jarne, Philippe; David, Patrice

2011-01-01

Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator–prey metacommunities with extinction–colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs. PMID:21367786

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.

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.

Transitions of tethered chain molecules under tension.

PubMed

Luettmer-Strathmann, Jutta; Binder, Kurt

2014-09-21

An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

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.

Production and characterization of murine models of classic and intermediate maple syrup urine disease

PubMed Central

Homanics, Gregg E; Skvorak, Kristen; Ferguson, Carolyn; Watkins, Simon; Paul, Harbhajan S

2006-01-01

Background Maple Syrup Urine Disease (MSUD) is an inborn error of metabolism caused by a deficiency of branched-chain keto acid dehydrogenase. MSUD has several clinical phenotypes depending on the degree of enzyme deficiency. Current treatments are not satisfactory and require new approaches to combat this disease. A major hurdle in developing new treatments has been the lack of a suitable animal model. Methods To create a murine model of classic MSUD, we used gene targeting and embryonic stem cell technologies to create a mouse line that lacked a functional E2 subunit gene of branched-chain keto acid dehydrogenase. To create a murine model of intermediate MSUD, we used transgenic technology to express a human E2 cDNA on the knockout background. Mice of both models were characterized at the molecular, biochemical, and whole animal levels. Results By disrupting the E2 subunit gene of branched-chain keto acid dehydrogenase, we created a gene knockout mouse model of classic MSUD. The homozygous knockout mice lacked branched-chain keto acid dehydrogenase activity, E2 immunoreactivity, and had a 3-fold increase in circulating branched-chain amino acids. These metabolic derangements resulted in neonatal lethality. Transgenic expression of a human E2 cDNA in the liver of the E2 knockout animals produced a model of intermediate MSUD. Branched-chain keto acid dehydrogenase activity was 5–6% of normal and was sufficient to allow survival, but was insufficient to normalize circulating branched-chain amino acids levels, which were intermediate between wildtype and the classic MSUD mouse model. Conclusion These mice represent important animal models that closely approximate the phenotype of humans with the classic and intermediate forms of MSUD. These animals provide useful models to further characterize the pathogenesis of MSUD, as well as models to test novel therapeutic strategies, such as gene and cellular therapies, to treat this devastating metabolic disease. PMID:16579849

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.

Communication: Polymer entanglement dynamics: Role of attractive interactions

DOE PAGES

Grest, Gary S.

2016-10-10

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. In this paper, using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect onmore » the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition T g. Finally, these results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.« less

The search for new amphiphiles: synthesis of a modular, high-throughput library

PubMed Central

Feast, George C; Lepitre, Thomas; Mulet, Xavier; Conn, Charlotte E; Hutt, Oliver E

2014-01-01

Summary Amphiphilic compounds are used in a variety of applications due to their lyotropic liquid-crystalline phase formation, however only a limited number of compounds, in a potentially limitless field, are currently in use. A library of organic amphiphilic compounds was synthesised consisting of glucose, galactose, lactose, xylose and mannose head groups and double and triple-chain hydrophobic tails. A modular, high-throughput approach was developed, whereby head and tail components were conjugated using the copper-catalysed azide–alkyne cycloaddition (CuAAC) reaction. The tails were synthesised from two core alkyne-tethered intermediates, which were subsequently functionalised with hydrocarbon chains varying in length and degree of unsaturation and branching, while the five sugar head groups were selected with ranging substitution patterns and anomeric linkages. A library of 80 amphiphiles was subsequently produced, using a 24-vial array, with the majority formed in very good to excellent yields. A preliminary assessment of the liquid-crystalline phase behaviour is also presented. PMID:25161714

The search for new amphiphiles: synthesis of a modular, high-throughput library.

PubMed

Feast, George C; Lepitre, Thomas; Mulet, Xavier; Conn, Charlotte E; Hutt, Oliver E; Savage, G Paul; Drummond, Calum J

2014-01-01

Amphiphilic compounds are used in a variety of applications due to their lyotropic liquid-crystalline phase formation, however only a limited number of compounds, in a potentially limitless field, are currently in use. A library of organic amphiphilic compounds was synthesised consisting of glucose, galactose, lactose, xylose and mannose head groups and double and triple-chain hydrophobic tails. A modular, high-throughput approach was developed, whereby head and tail components were conjugated using the copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction. The tails were synthesised from two core alkyne-tethered intermediates, which were subsequently functionalised with hydrocarbon chains varying in length and degree of unsaturation and branching, while the five sugar head groups were selected with ranging substitution patterns and anomeric linkages. A library of 80 amphiphiles was subsequently produced, using a 24-vial array, with the majority formed in very good to excellent yields. A preliminary assessment of the liquid-crystalline phase behaviour is also presented.

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.

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)

Dynamics of Entangled Polymers: Role of Attractive Interactions

NASA Astrophysics Data System (ADS)

Grest, Gary S.; Koski, Jason

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. Numerical simulations of highly coarse grained models are often used to follow chain mobility from the intermediate Rouse and reptation regimes to the late time diffusive regime. In these models, purely repulsive interactions between monomers are typically used because it is less computationally expensive than including attractive interactions. The effect of including the attractive interaction on the local and macroscopic properties of entangled polymer melts is explored over a wide temperature range using large scale molecular dynamics simulations. Attractive interactions are shown to have little effect on the local packing for all temperatures T and chain mobility for T higher than about twice the glass transition Tg. For lower T, the attractive interactions play a significant role, reducing the chain mobility compared to the repulsive case. As T approaches Tg breakdown of time-temperature superposition for the stress autocorrelation function is observed. Sandia National Labs is a multiprogram laboratory managed and operated by Sandia Corporation, a Lockheed-Martin Company, for the U.S. Dept of Energy under Contract No. DEAC04-94AL85000.

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

Greatly Suppressed Shuttle Effect for Improved Lithium Sulfur Battery Performance through Short Chain Intermediates.

PubMed

Xu, Na; Qian, Tao; Liu, Xuejun; Liu, Jie; Chen, Yu; Yan, Chenglin

2017-01-11

The high solubility of long-chain lithium polysulfides and their infamous shuttle effect in lithium sulfur battery lead to rapid capacity fading along with low Coulombic efficiency. To address above issues, we propose a new strategy to suppress the shuttle effect for greatly enhanced lithium sulfur battery performance mainly through the formation of short-chain intermediates during discharging, which allows significant improvements including high capacity retention of 1022 mAh/g with 87% retention for 450 cycles. Without LiNO 3 -containing electrolytes, the excellent Coulombic efficiency of ∼99.5% for more than 500 cycles is obtained, suggesting the greatly suppressed shuttle effect. In situ UV/vis analysis of electrolyte during cycling reveals that the short-chain Li 2 S 2 and Li 2 S 3 polysulfides are detected as main intermediates, which are theoretically verified by density functional theory (DFT) calculations. Our strategy may open up a new avenue for practical application of lithium sulfur battery.

Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides.

PubMed

Uribe, Lalita; Gauss, Jürgen; Diezemann, Gregor

2015-07-02

Using molecular simulations, we analyze the unfolding pathways of various peptides. We compare the mechanical unfolding of a β-alanine's octamer (β-HAla8) and an α-alanine's decamer (α-Ala10). Using force-probe molecular-dynamics simulations, to induce unfolding, we show that the 3(14)-helix formed by β-HAla8 is mechanically more stable than the α-helix formed by α-Ala10, although both structures are stabilized by six hydrogen bonds. Additionally, computations of the potential of mean force validate this result and show that also the thermal stability of the 3(14)-helix is higher. It is demonstrated that β-HAla8 unfolds in a two-step fashion with a stable intermediate. This is contrasted with the known single-step scenario of the unfolding of α-Ala10. Furthermore, we present a study of the chain-length dependence of the mechanical unfolding pathway of the 3(14)-helix. The calculation of the dynamic strength for oligomers with chain lengths ranging from 6 to 18 monomers shows that the unfolding pathway of helices with an integer and noninteger number of turns has m + 1 and m energy barriers, respectively, with m being the number of complete turns. The additional barrier for helices with an integer number of turns is shown to be related to the breaking of the N-terminus' hydrogen bond.

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

Polymer diffusion in quenched disorder: A renormalization group approach

NASA Astrophysics Data System (ADS)

Ebert, Ute

1996-01-01

We study the diffusion of polymers through quenched short-range correlated random media by renormalization group (RG) methods, which allow us to derive universal predictions in the limit of long chains and weak disorder. We take local quenched random potentials with second moment v and the excluded-volume interaction u of the chain segments into account. We show that our model contains the relevant features of polymer diffusion in random media in the RG sense if we focus on the local entropic effects rather than on the topological constraints of a quenched random medium. The dynamic generating functional and the general structure of its perturbation expansion in u and v are derived. The distribution functions for the center-of-mass motion and the internal modes of one chain and for the correlation of the center of mass motions of two chains are calculated to one-loop order. The results allow for sufficient cross-checks to have trust in the one-loop renormalizability of the model. The general structure as well as the one-loop results of the integrated RG flow of the parameters are discussed. Universal results can be found for the effective static interaction w≔u-v≥0 and for small effective disorder couplingbar v(l) on the intermediate length scale l. As a first physical prediction from our analysis, we determine the general nonlinear scaling form of the chain diffusion constant and evaluate it explicitly as[Figure not available: see fulltext.] forbar v(l) ≪ 1.

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.

The degradation of bioactive peptides and proteins by dipeptidyl peptidase IV from human placenta.

PubMed

Nausch, I; Mentlein, R; Heymann, E

1990-11-01

The degradation of several bioactive peptides and proteins by purified human dipeptidyl peptidase IV is reported. It was hitherto unknown that human gastrin-releasing peptide, human chorionic gonadotropin, human pancreatic polypeptide, sheep prolactin, aprotinin, corticotropin-like intermediate lobe peptide and (Tyr-)melanostatin are substrates of this peptidase. Kinetic constants were determined for the degradation of a number of other natural peptides, including substance P, the degradation of which has been described earlier in a qualitative manner. Generally, small peptides are degraded much more rapidly than proteins. However, the Km-values seem to be independent of the peptide chain length. The influence of the action of dipeptidyl peptidase IV on the biological function of peptides and proteins is discussed.

Study of the chain conformation of thermotropic nematic main chain polyesters

NASA Astrophysics Data System (ADS)

Li, M. H.; Brûlet, A.; Cotton, J. P.; Davidson, P.; Strazielle, C.; Keller, P.

1994-10-01

The conformation of main chain mesomorphic polyesters is studied by small angle neutron scattering (SANS) in the isotropic and in the nematic phases, by using mixtures of deuterated and undeuterated polymers. Particular attention is given to neglect the transesterification effects occurring mainly at high temperature for these LC polymers. In the isotropic phase, despite the presence of long rigid mesogenic groups, the LC polyester chains have a Gaussian conformation shown by the variation of the radius of gyration as a function of the molecular weight. This result is confirmed from the scattering variation in the intermediate range of the scattering vector. In the nematic phase, the SANS data are well fitted to a model of cylinder, in which the main chain polymer is confined. In the unoriented phase, the measurements in the intermediate range give the values of the radii of cylinders : they lie in between 10 Å and 19 Å depending on the degree of polymerization of chains. In the oriented nematic phase, the scattering patterns are highly anisotropic : they correspond to very long, thin and well-oriented cylinders. We have calculated the fully extended chain lengths using for the monomer length that measured in situ by X-ray diffraction. Then the comparison of this length with the measured height of the cylinders gives the existence of hairpins and their number per chain. For the short chain, the conformation is almost completely elongated in the nematic direction, whereas hairpin defects appear in longer chains. Their number decreases slightly with decreasing temperature. The orientational fluctuations of cylinders relatively to the nematic director are weak as shown from the high values of their order parameter (P_2 > 0.9). These results are discussed for two spacer lengths as a function of the molecular weight and of the temperature. La conformation de polyesters linéaires mésomorphes est étudiée par diffusion de neutrons aux petits angles (DNPA) dans les phases isotrope et nématique sur des mélanges de polymères hydrogénés et deutériés. Les conditions expérimentales ont été choisies afin de pouvoir négliger les effets de la transestérification obtenus à haute température avec cette famille de polymères cristaux liquides. Dans la phase isotrope, en dépit de la présence de longs et rigides groupements mésogènes, les chaînes de polymères ont une conformation gaussienne, comme le montre la variation du rayon de giration en fonction de la masse moléculaire. Ce résultat est confirmé par les mesures faites dans le domaine intermédiaire du vecteur de diffusion. Dans la phase nématique, les données de DNPA sont bien ajustées par un modèle de cylindre dans lequel la chaîne de polymère est confinée. Dans la phase non orientée, les mesures faites dans le domaine intermédiaire donnent les valeurs des rayons des cylindres (compris entre 10 Å et 19 Å selon le degré de polymérisation des chaînes). Dans la phase nématique orientée, les figures de diffusion sont très anisotropes et correspondent à de longs et étroits cylindres bien orientés. La longueur de la chaîne totalement étirée est calculée à partir de la longueur du monomère mesurée par diffraction de rayons X. Par comparaison avec la hauteur du cylindre mesurée en DNPA, nous déduisons l'existence des épingles à cheveux et leur nombre par chaîne. La conformation d'une chaîne courte est complètement étirée dans la direction du champ nématique, alors que des défauts du type épingles à cheveux apparaissent dans les chaînes plus longues. Le nombre de ces défauts décroît légèrement en diminuant la température. Les fluctuations d'orientation des cylindres autour de la direction du champ nématique sont faibles comme le montrent les valeurs élevées des paramètres d'ordre des cylindres (P_2 > 0,9). Les résultats sont discutés, pour deux longueurs d'espaceur, en fonction de la masse moléculaire et de la température.

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.

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

PubMed

Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

2011-08-01

The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

Small angle neutron scattering (SANS) study of gastric mucin solutions

NASA Astrophysics Data System (ADS)

Hong, Z.; Bansil, R.; Waigh, T.; Turner, B.; Bhaskar, K. R.; Afdhal, N.; Lal, J.

2002-03-01

We report the first results from a SANS study of purified porcine gastric mucin solutions in D2O. The ability of this glycoprotein to protect the stomach epithelium from acid damage, may be due to a pH dependent conformational transition which leads to gelation at low pH Cao et. al. (Biophysical. J. 76, 1250, 1999). SANS measurements were made over the concentration range of 1 -15 mg/ml at pH 7, 4 and 2. The data indicate that at pH 7 the excluded volume exponent is 1.7, characteristic of swollen chains whereas at pH 2 this exponent increases to 2, indicating theta or poor solvent conditions, consistent with the hydrophobic interactions increasing at lower pH. From a Guinier analysis of the 1mg/ml data at low q's (0.003- 0.007 Å-1) we estimate the cross section radius of the effective cylinder to be 23nm and its length as 96nm in an unbuffered sample, i.e. close to pH 7. In the intermediate q-range (0.01 -0.1Å-1) at pH 7 a fit to the Debye chain gives radius of gyration Rg of 16nm. Mucin is best modelled as an elongated micelle with a cylindrical or worm-like chain to represent the protein core and the sugar chains forming the corona. Results of such calculations will be presented.

(13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

PubMed

Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

2015-12-03

Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate.

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.

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.

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.

[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).

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.

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.

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

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.

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.

Evolution of complex life cycles in trophically transmitted helminths. I. Host incorporation and trophic ascent.

PubMed

Parker, G A; Ball, M A; Chubb, J C

2015-02-01

Links between parasites and food webs are evolutionarily ancient but dynamic: life history theory provides insights into helminth complex life cycle origins. Most adult helminths benefit by sexual reproduction in vertebrates, often high up food chains, but direct infection is commonly constrained by a trophic vacuum between free-living propagules and definitive hosts. Intermediate hosts fill this vacuum, facilitating transmission to definitive hosts. The central question concerns why sexual reproduction, and sometimes even larval growth, is suppressed in intermediate hosts, favouring growth arrest at larval maturity in intermediate hosts and reproductive suppression until transmission to definitive hosts? Increased longevity and higher growth in definitive hosts can generate selection for larger parasite body size and higher fecundity at sexual maturity. Life cycle length is increased by two evolutionary mechanisms, upward and downward incorporation, allowing simple (one-host) cycles to become complex (multihost). In downward incorporation, an intermediate host is added below the definitive host: models suggest that downward incorporation probably evolves only after ecological or evolutionary perturbations create a trophic vacuum. In upward incorporation, a new definitive host is added above the original definitive host, which subsequently becomes an intermediate host, again maintained by the trophic vacuum: theory suggests that this is plausible even under constant ecological/evolutionary conditions. The final cycle is similar irrespective of its origin (upward or downward). Insights about host incorporation are best gained by linking comparative phylogenetic analyses (describing evolutionary history) with evolutionary models (examining selective forces). Ascent of host trophic levels and evolution of optimal host taxa ranges are discussed. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Effect of acute feeding of diets of varying fatty acid composition on intestinal apolipoprotein expression in the newborn swine.

PubMed

Wang, H; Zhan, R; Hunter, F; Du, J; Black, D

1996-06-01

The purpose of this study was to determine the effects of dietary fatty acids of varying chain lengths and degrees of saturation on intestinal apolipoprotein (apo) B and A-I expression in the newborn piglet. Two-day-old female piglets received one of three isocaloric formulas containing 48% of total calories (120 kcal/kg/24 h) as medium-chain triglycerides (MCT) from MCT oil, intermediate-chain saturated triglycerides (ICST) from coconut oil, or long-chain polyunsaturated triglycerides (LCPUT) from safflower oil by continuous duodenal infusion for 24 h. After in situ radiolabeling, jejunal and ileal mucosal apo B-48 and A-I were immunoprecipitated, and synthesis was expressed as percentage of total protein synthesis. Mucosal apo B and A-I mass was measured by ELISA as nanograms of apoprotein/microgram of total protein. Fifty percent less apo B jejunal synthesis was present in the ICST group versus the MCT and LCPUT groups (0.67 +/- 0.07, 1.19 +/- 0.20, and 1.25 +/- 0.15, respectively, mean +/- SEM, p < 0.05). Jejunal apo B mass was lower in the MCT group versus the ICST and LCPUT groups (0.10 +/- 0.02, 0.21 +/- 0.03, and 0.16 +/- 0.03, respectively, p < 0.05). Ileal apo B synthesis was lowest in the ICST group. No differences were found in ileal apo B mass. Two-fold higher jejunal apo A-I synthesis was found in the LCPUT group versus the MCT and ICST groups (14.18 +/- 1.69, 7.56 +/- 2.63, and 6.36 +/- 0.58, respectively, p < 0.01). No differences were found for jejunal apo A-I mass. In the ileum, the only difference was a higher apo A-I mass in the LCPUT group (p < 0.05). We conclude that in the newborn piglet intestinal apo B and A-I expression is acutely and differentially regulated by dietary lipid varying in fatty acid chain length and saturation. The patterns of regulation are complex and vary among specific apolipoproteins and regions of the small intestine and include co- and posttranslational mechanisms.

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

Semisynthetic protein nanoreactor for single-molecule chemistry

PubMed Central

Lee, Joongoo; Bayley, Hagan

2015-01-01

The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach. PMID:26504203

Tunable Assembly of Gold Nanorods in Polymer Solutions To Generate Controlled Nanostructured Materials

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

Poling-Skutvik, Ryan; Lee, Jonghun; Narayanan, Suresh

In this study, gold nanorods grafted with short chain polymers are assembled into controlled open structures using polymer-induced depletion interactions and structurally characterized using small angle x-ray scattering. When the nanorod diameter is smaller than the radius of gyration of the depletant polymer, the depletion interaction depends solely on the correlation length of the polymer solution and not directly on the polymer molecular weight. As the polymer concentration increases, the stronger depletion interactions increasingly compress the grafted chains and push the gold nanorods closer together. By contrast, other structural characteristics such as the number of nearest neighbors and fractal dimensionmore » exhibit a non-monotonic dependence on polymer concentration. These parameters are maximal at intermediate concentrations, which are attributed to a crossover from reaction-limited to diffusion-limited aggregation. Finally, the control over structural properties of anisotropic nanoscale building blocks demonstrated here will be beneficial to designing and producing materials in situ with specific direction-dependent nanoscale properties and provides a crucial route for advances in additive manufacturing.« less

Tunable Assembly of Gold Nanorods in Polymer Solutions To Generate Controlled Nanostructured Materials

DOE PAGES

Poling-Skutvik, Ryan; Lee, Jonghun; Narayanan, Suresh; ...

2018-01-17

In this study, gold nanorods grafted with short chain polymers are assembled into controlled open structures using polymer-induced depletion interactions and structurally characterized using small angle x-ray scattering. When the nanorod diameter is smaller than the radius of gyration of the depletant polymer, the depletion interaction depends solely on the correlation length of the polymer solution and not directly on the polymer molecular weight. As the polymer concentration increases, the stronger depletion interactions increasingly compress the grafted chains and push the gold nanorods closer together. By contrast, other structural characteristics such as the number of nearest neighbors and fractal dimensionmore » exhibit a non-monotonic dependence on polymer concentration. These parameters are maximal at intermediate concentrations, which are attributed to a crossover from reaction-limited to diffusion-limited aggregation. Finally, the control over structural properties of anisotropic nanoscale building blocks demonstrated here will be beneficial to designing and producing materials in situ with specific direction-dependent nanoscale properties and provides a crucial route for advances in additive manufacturing.« less

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.

Alcohol's Effects on Lipid Bilayer Properties

PubMed Central

Ingólfsson, Helgi I.; Andersen, Olaf S.

2011-01-01

Alcohols are known modulators of lipid bilayer properties. Their biological effects have long been attributed to their bilayer-modifying effects, but alcohols can also alter protein function through direct protein interactions. This raises the question: Do alcohol's biological actions result predominantly from direct protein-alcohol interactions or from general changes in the membrane properties? The efficacy of alcohols of various chain lengths tends to exhibit a so-called cutoff effect (i.e., increasing potency with increased chain length, which that eventually levels off). The cutoff varies depending on the assay, and numerous mechanisms have been proposed such as: limited size of the alcohol-protein interaction site, limited alcohol solubility, and a chain-length-dependent lipid bilayer-alcohol interaction. To address these issues, we determined the bilayer-modifying potency of 27 aliphatic alcohols using a gramicidin-based fluorescence assay. All of the alcohols tested (with chain lengths of 1–16 carbons) alter the bilayer properties, as sensed by a bilayer-spanning channel. The bilayer-modifying potency of the short-chain alcohols scales linearly with their bilayer partitioning; the potency tapers off at higher chain lengths, and eventually changes sign for the longest-chain alcohols, demonstrating an alcohol cutoff effect in a system that has no alcohol-binding pocket. PMID:21843475

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.

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.

Substrate Trapping in Crystals of the Thiolase OleA Identifies Three Channels That Enable Long Chain Olefin Biosynthesis*

PubMed Central

Goblirsch, Brandon R.; Jensen, Matthew R.; Mohamed, Fatuma A.; Wackett, Lawrence P.; Wilmot, Carrie M.

2016-01-01

Phylogenetically diverse microbes that produce long chain, olefinic hydrocarbons have received much attention as possible sources of renewable energy biocatalysts. One enzyme that is critical for this process is OleA, a thiolase superfamily enzyme that condenses two fatty acyl-CoA substrates to produce a β-ketoacid product and initiates the biosynthesis of long chain olefins in bacteria. Thiolases typically utilize a ping-pong mechanism centered on an active site cysteine residue. Reaction with the first substrate produces a covalent cysteine-thioester tethered acyl group that is transferred to the second substrate through formation of a carbon-carbon bond. Although the basics of thiolase chemistry are precedented, the mechanism by which OleA accommodates two substrates with extended carbon chains and a coenzyme moiety—unusual for a thiolase—are unknown. Gaining insights into this process could enable manipulation of the system for large scale olefin production with hydrocarbon chains lengths equivalent to those of fossil fuels. In this study, mutagenesis of the active site cysteine in Xanthomonas campestris OleA (Cys143) enabled trapping of two catalytically relevant species in crystals. In the resulting structures, long chain alkyl groups (C12 and C14) and phosphopantetheinate define three substrate channels in a T-shaped configuration, explaining how OleA coordinates its two substrates and product. The C143A OleA co-crystal structure possesses a single bound acyl-CoA representing the Michaelis complex with the first substrate, whereas the C143S co-crystal structure contains both acyl-CoA and fatty acid, defining how a second substrate binds to the acyl-enzyme intermediate. An active site glutamate (Gluβ117) is positioned to deprotonate bound acyl-CoA and initiate carbon-carbon bond formation. PMID:27815501

Substrate Trapping in Crystals of the Thiolase OleA Identifies Three Channels That Enable Long Chain Olefin Biosynthesis

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

Goblirsch, Brandon R.; Jensen, Matthew R.; Mohamed, Fatuma A.

Phylogenetically diverse microbes that produce long chain, olefinic hydrocarbons have received much attention as possible sources of renewable energy biocatalysts. One enzyme that is critical for this process is OleA, a thiolase superfamily enzyme that condenses two fatty acyl-CoA substrates to produce a β-ketoacid product and initiates the biosynthesis of long chain olefins in bacteria. Thiolases typically utilize a ping-pong mechanism centered on an active site cysteine residue. Reaction with the first substrate produces a covalent cysteine-thioester tethered acyl group that is transferred to the second substrate through formation of a carbon-carbon bond. Although the basics of thiolase chemistry aremore » precedented, the mechanism by which OleA accommodates two substrates with extended carbon chains and a coenzyme moiety—unusual for a thiolase—are unknown. Gaining insights into this process could enable manipulation of the system for large scale olefin production with hydrocarbon chains lengths equivalent to those of fossil fuels. In this study, mutagenesis of the active site cysteine in Xanthomonas campestris OleA (Cys143) enabled trapping of two catalytically relevant species in crystals. In the resulting structures, long chain alkyl groups (C12 and C14) and phosphopantetheinate define three substrate channels in a T-shaped configuration, explaining how OleA coordinates its two substrates and product. The C143A OleA co-crystal structure possesses a single bound acyl-CoA representing the Michaelis complex with the first substrate, whereas the C143S co-crystal structure contains both acyl-CoA and fatty acid, defining how a second substrate binds to the acyl-enzyme intermediate. An active site glutamate (Gluβ117) is positioned to deprotonate bound acyl-CoA and initiate carbon-carbon bond formation.« less

Size determination of bacterial capsular oligosaccharides used to prepare conjugate vaccines.

PubMed

Ravenscroft, N; Averani, G; Bartoloni, A; Berti, S; Bigio, M; Carinci, V; Costantino, P; D'Ascenzi, S; Giannozzi, A; Norelli, F; Pennatini, C; Proietti, D; Ceccarini, C; Cescutti, P

1999-07-16

We recently described the use of ion exchange chromatography for analysis and the industrial scale preparation of pools of oligosaccharides of intermediate chain length from polysaccharides of Haemophilus influenzae type b (Hib) and Neisseria meningitidis groups A and C. These negatively charged "sized" oligosaccharides are activated and conjugated to the carrier protein (CRM197) to prepare the corresponding glycoconjugate vaccines. Characterization and accurate determination of the degree of polymerization (DP) of the pool of oligosaccharides is essential for the consistent production of these conjugate vaccines. This paper describes the colorimetric assays used for determination of the average DP of the Hib and meningococcal oligosaccharides, and the qualification of these assays achieved by size characterization of the respective oligosaccharides by use of physicochemical methods, including liquid chromatography, mass spectrometry (ionspray) and NMR spectroscopy.

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

Pemble,C.; Johnson, L.; Kridel, S.

Human fatty acid synthase (FAS) is uniquely expressed at high levels in many tumor types. Pharmacological inhibition of FAS therefore represents an important therapeutic opportunity. The drug Orlistat, which has been approved by the US Food and Drug Administration, inhibits FAS, induces tumor cell-specific apoptosis and inhibits the growth of prostate tumor xenografts. We determined the 2.3-{angstrom}-resolution crystal structure of the thioesterase domain of FAS inhibited by Orlistat. Orlistat was captured in the active sites of two thioesterase molecules as a stable acyl-enzyme intermediate and as the hydrolyzed product. The details of these interactions reveal the molecular basis for inhibitionmore » and suggest a mechanism for acyl-chain length discrimination during the FAS catalytic cycle. Our findings provide a foundation for the development of new cancer drugs that target FAS.« less

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

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

SIMULATION FROM ENDPOINT-CONDITIONED, CONTINUOUS-TIME MARKOV CHAINS ON A FINITE STATE SPACE, WITH APPLICATIONS TO MOLECULAR EVOLUTION.

PubMed

Hobolth, Asger; Stone, Eric A

2009-09-01

Analyses of serially-sampled data often begin with the assumption that the observations represent discrete samples from a latent continuous-time stochastic process. The continuous-time Markov chain (CTMC) is one such generative model whose popularity extends to a variety of disciplines ranging from computational finance to human genetics and genomics. A common theme among these diverse applications is the need to simulate sample paths of a CTMC conditional on realized data that is discretely observed. Here we present a general solution to this sampling problem when the CTMC is defined on a discrete and finite state space. Specifically, we consider the generation of sample paths, including intermediate states and times of transition, from a CTMC whose beginning and ending states are known across a time interval of length T. We first unify the literature through a discussion of the three predominant approaches: (1) modified rejection sampling, (2) direct sampling, and (3) uniformization. We then give analytical results for the complexity and efficiency of each method in terms of the instantaneous transition rate matrix Q of the CTMC, its beginning and ending states, and the length of sampling time T. In doing so, we show that no method dominates the others across all model specifications, and we give explicit proof of which method prevails for any given Q, T, and endpoints. Finally, we introduce and compare three applications of CTMCs to demonstrate the pitfalls of choosing an inefficient sampler.

Phenylalanine 445 within oxidosqualene-lanosterol cyclase from Saccharomyces cerevisiae influences C-Ring cyclization and deprotonation reactions.

PubMed

Wu, Tung-Kung; Liu, Yuan-Ting; Chiu, Feng-Hsuan; Chang, Cheng-Hsiang

2006-10-12

[reaction: see text] We describe the Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase Phe445 site-saturated mutants that generate truncated tricyclic and altered deprotonation product profiles. Among these mutants, only polar side-chain group substitutions genetically complemented yeast viability and produced spatially related product diversity, supporting the Johnson model that cation-pi interactions between a carbocationic intermediate and an enzyme can be replaced by an electrostatic or polar side chain to stabilize the cationic intermediate, but with product differentiation.

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.

Topological structure and mechanics of glassy polymer networks.

PubMed

Elder, Robert M; Sirk, Timothy W

2017-11-22

The influence of chain-level network architecture (i.e., topology) on mechanics was explored for unentangled polymer networks using a blend of coarse-grained molecular simulations and graph-theoretic concepts. A simple extension of the Watts-Strogatz model is proposed to control the graph properties of the network such that the corresponding physical properties can be studied with simulations. The architecture of polymer networks assembled with a dynamic curing approach were compared with the extended Watts-Strogatz model, and found to agree surprisingly well. The final cured structures of the dynamically-assembled networks were nearly an intermediate between lattice and random connections due to restrictions imposed by the finite length of the chains. Further, the uni-axial stress response, character of the bond breaking, and non-affine displacements of fully-cured glassy networks were analyzed as a function of the degree of disorder in the network architecture. It is shown that the architecture strongly affects the network stability, flow stress, onset of bond breaking, and ultimate stress while leaving the modulus and yield point nearly unchanged. The results show that internal restrictions imposed by the network architecture alter the chain-level response through changes to the crosslink dynamics in the flow regime and through the degree of coordinated chain failure at the ultimate stress. The properties considered here are shown to be sensitive to even incremental changes to the architecture and, therefore, the overall network architecture, beyond simple defects, is predicted to be a meaningful physical parameter in the mechanics of glassy polymer networks.

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.

Quantifying Short-Chain Chlorinated Paraffin Congener Groups.

PubMed

Yuan, Bo; Bogdal, Christian; Berger, Urs; MacLeod, Matthew; Gebbink, Wouter A; Alsberg, Tomas; de Wit, Cynthia A

2017-09-19

Accurate quantification of short-chain chlorinated paraffins (SCCPs) poses an exceptional challenge to analytical chemists. SCCPs are complex mixtures of chlorinated alkanes with variable chain length and chlorination level; congeners with a fixed chain length (n) and number of chlorines (m) are referred to as a "congener group" C n Cl m . Recently, we resolved individual C n Cl m by mathematically deconvolving soft ionization high-resolution mass spectra of SCCP mixtures. Here we extend the method to quantifying C n Cl m by introducing C n Cl m specific response factors (RFs) that are calculated from 17 SCCP chain-length standards with a single carbon chain length and variable chlorination level. The signal pattern of each standard is measured on APCI-QTOF-MS. RFs of each C n Cl m are obtained by pairwise optimization of the normal distribution's fit to the signal patterns of the 17 chain-length standards. The method was verified by quantifying SCCP technical mixtures and spiked environmental samples with accuracies of 82-123% and 76-109%, respectively. The absolute differences between calculated and manufacturer-reported chlorination degrees were -0.9 to 1.0%Cl for SCCP mixtures of 49-71%Cl. The quantification method has been replicated with ECNI magnetic sector MS and ECNI-Q-Orbitrap-MS. C n Cl m concentrations determined with the three instruments were highly correlated (R 2 > 0.90) with each other.

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.

Precise low cost chain gears for heliostats

NASA Astrophysics Data System (ADS)

Liedke, Phillip; Lewandowski, Arkadiusz; Pfahl, Andreas; Hölle, Erwin

2016-05-01

This work investigates the potential of chain gears as precise and low cost driving systems for rim drive heliostats. After explaining chain gear basics the polygon effect and chain lengthening are investigated. The polygon effect could be measured by a heliostat with chain rim gear and the chain lengthening with an accordant test set up. Two gear stages are scope of this work: a rim gear and an intermediate gear. Dimensioning, pretensioning and designing for both stages are explained.

Identification of immunodominant epitopes of alpha-crystallins recognized by antibodies in sera of patients with uveitis.

PubMed

Doycheva, Deshka; Preuss, Beate; Deuter, Christoph; Zierhut, Manfred; Klein, Reinhild

2012-02-01

A high incidence of autoantibodies to lens proteins has been found in sera of patients with uveitis. We showed previously that the anti-lens antibodies reacted predominantly with α-crystallins. The aim of the present study was to identify immunodominant epitopes within the protein chains of human αA- and αB-crystallin. Epitope specificities of antibodies to αA- and αB-crystallin were examined by ELISA using synthetic overlapping peptides, spanning the entire length of both α-crystallins. The peptides consisted of 25 amino acid residues, with an overlap of at least eight amino acids each. The synthetic peptides were tested against sera of 110 patients with different uveitis forms, classified according to anatomical location of intraocular inflammation. Four immunodominant regions within the protein chains of αA- and αB-crystallin could be identified. These regions were recognized by antibodies in sera of 56% of uveitis patients. Anti-lens antibodies of IgG-type reacted preferentially with regions located at amino acid (aa) residues aa:69-93 and aa:137-161 of αA-crystallin as well as aa:69-110 and aa:137-161 of αB-crystallin. IgM antibodies recognized predominantly region aa:149-173 of αA-crystallin, and aa:69-110 and aa:151-175 of αB-crystallin. IgM antibodies directed to peptide aa:69-93 of αB-crystallin were found in sera of 30% of patients with intermediate uveitis. Four immunodominant B-cell epitopes within the protein chains of αA- and αB-crystallin have been identified; however, no clear correlation with the anatomically defined uveitis subtypes has been found except for intermediate uveitis. Whether there may be a correlation with uveitis forms with similar etiopathogenesis has to be evaluated in further studies.

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.

Quantitative ‘Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids

PubMed Central

Fu, Jilagamazhi; Sharma, Parveen; Spicer, Vic; Krokhin, Oleg V.; Zhang, Xiangli; Fristensky, Brian; Cicek, Nazim; Sparling, Richard; Levin, David. B.

2015-01-01

Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. ‘Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the ‘Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the monomer composition of mcl-PHA polymers. Understanding the relationships between genome content, gene and gene product expression, and how these factors influence polymer synthesis, will aid in optimization of mcl-PHA production by P. putida LS46 using biodiesel waste streams. PMID:26544181

Microscopic theory for dynamics in entangled polymer nanocomposites

NASA Astrophysics Data System (ADS)

Yamamoto, Umi

New microscopic theories for describing dynamics in polymer nanocomposites are developed and applied. The problem is addressed from two distinct perspectives and using two different theoretical approaches. The first half of this dissertation studies the long-time and intermediate-time dynamics of nanoparticles in entangled and unentangled polymer melts for dilute particle concentrations. Using a combination of mode-coupling, Brownian motion, and polymer physics ideas, the nanoparticle long-time diffusion coefficients is formulated in terms of multiple length-scales, packing microstructures, and spatially-resolved polymer density fluctuation dynamics. The key motional mechanism is described via the parallel relaxation of the force exerted on the particle controlled by collective polymer constraint-release and the particle self-motion. A sharp but smooth crossover from the hydrodynamic to the non-hydrodynamic regime is predicted based on the Stokes-Einstein violation ratio as a function of all the system variables. Quantitative predictions are made for the recovery of the Stokes-Einstein law, and the diffusivity in the crossover regime agrees surprisingly well with large-scale molecular dynamics simulations for all particle sizes and chain lengths studied. The approach is also extended to address intermediate-time anomalous transport of a single nanoparticle and two-particle relative diffusion. The second half of this dissertation focuses on developing a novel dynamical theory for a liquid of infinitely-thin rods in the presence of hard spherical obstacles, aiming at a technical and conceptual extension of the existing paradigm for entangled polymer dynamics. As a fundamental theoretical development, the two-component generalization of a first-principles dynamic meanfield approach is presented. The theory enforces inter-needle topological uncrossability and needlesphere impenetrability in a unified manner, leading to a generalized theory of entanglements that includes the sphere excluded volume effect. Coupled self-consistent equations for the generalized diffusion tensors are constructed, and the expressions for the transverse localization lengths and the long-time diffusion coefficients are derived. In the static sphere limit, we find the effective tube diameter is generally reduced as a function of a single confinement parameter that quantifies the number of particles penetrating into the pure-polymer tube. A preliminary extension to treat flexible chain melts has also been achieved, and shown to agree reasonably well with simulations. The anisotropic needle diffusion constants are rich functions of the length-scale ratios, needle concentration and particle volume fraction. We show that the steric blocking of the longitudinal motion causes a literal and simultaneous localization of the two diffusion channels, and entangled needles can diffuse via a modified reptation dynamics over a window of polymer concentration but the compression of the tube and the blocking of the reptation motion must be accounted for. Generalization to treat mobile spheres is also possible and fully formulated.

Regioselective intramolecular Pauson-Khand reactions of C60: an electrochemical study and theoretical underpinning.

PubMed

Martín, Nazario; Altable, Margarita; Filippone, Salvatore; Martín-Domenech, Angel; Poater, Albert; Solà, Miquel

2005-04-22

Suitably functionalized fulleropyrrolidines endowed with one or two propargyl groups at the C-2 position of the pyrrolidine ring (1,6-enynes) react efficiently and regioselectively with [Co2(CO)8] to afford the respective Pauson-Khand products with an unprecedented three (5 a-d, 7, and 24) or five (25) pentagonal rings, respectively, fused onto the fullerene sphere. Fulleropyrrolidines with 1,7-, 1,9-, 1,10-, or 1,11-enyne moieties do not undergo the PK reaction and, instead, the intermediate dicobalt complexes formed with the alkynyl group are isolated in quantitative yields. These differences in reactivity have been studied by DFT calculations with a generalized gradient approximation (GGA) functional and several important energy and structural differences were found for the intermediates formed by the interaction between the coordinatively unsaturated Co atom and the pi system of C60 in 1,6- and 1,7-enynes. The different lengths of the alkyne chains are responsible for the observed reactivities. Cyclic voltammetry reveals that the presence of the cyclopentenone's carbonyl group connected directly to the C60 core results in PK compounds with remarkable electron-accepting ability.

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.

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

Metabolic reconstructions identify plant 3-methylglutaconyl-CoA hydratase that is crucial for branched-chain amino acid catabolism in mitochondria

USDA-ARS?s Scientific Manuscript database

The proteinogenic branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are essential nutrients for mammals. In plants, they double as alternative energy sources when carbohydrates become limiting, the catabolism of BCAAs providing electrons to the respiratory chain and intermediates...

cDNA cloning and characterization of Type I procollagen alpha1 chain in the skate Raja kenojei.

PubMed

Hwang, Jae-Ho; Yokoyama, Yoshihiro; Mizuta, Shoshi; Yoshinaka, Reiji

2006-05-01

A full-length cDNA of the Type I procollagen alpha1 [pro-alpha1(I)] chain (4388 bp), coding for 1463 amino acid residues in the total length, was determined by RACE PCR using a cDNA library constructed from 4-week embryo of the skate Raja kenojei. The helical region of the skate pro-alpha1(I) chain consisted of 1014 amino acid residues - the same as other fibrillar collagen alpha chains from higher vertebrates. Comparison on denaturation temperatures of Type I collagens from the skate, rainbow trout (Oncorhynchus mykiss) and rat (Rattus norvegicus) revealed that the number of Gly-Pro-Pro and Gly-Gly in the alpha1(I) chains could be directly related to the thermal stability of the helix. The expression property of the skate pro-alpha1(I) chain mRNA and phylogenetic analysis with other vertebrate pro-alpha1(I) chains suggested that skate pro-alpha1(I) chain could be a precursor form of the skate Type I collagen alpha1 chain. The present study is the first evidence for the primary structure of full-length pro-alpha1(I) chain in an elasmobranch.

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.

Chain length effects of p-oligophenyls with comparison of benzene by Raman scattering

NASA Astrophysics Data System (ADS)

Zhang, Kai; Chen, Xiao-Jia

2018-02-01

Raman scattering measurements are performed on benzene and a number of p-oligophenyls including biphenyl, p-terphenyl, p-quaterphenyl, p-quinquephenyl, and p-sexiphenyl at ambient conditions. The vibrational modes of the intra- and intermolecular terms in these materials are analyzed and compared. Chain length effects on the vibrational properties are examined for the C-H in-plane bending mode and the inter-ring C-C stretching mode at around 1200 cm-1 and 1280 cm-1, respectively, and the C-C stretching modes at around 1600 cm-1. The complex and fluctuating properties of these modes result in an imprecise estimation of the chain length of these molecules. Meanwhile, the obtained ratio of the intensities of the 1200 cm-1 mode and 1280 cm-1 mode is sensitive to the applied lasers. A librational motion mode with the lowest energy is found to have a monotonous change with the increase in the chain length. This mode is simply relevant to the c axis of the unit cell. Such an obvious trend makes it a better indicator for determining the chain length effects on the physical and chemical properties in these molecules.

The cellular level of O-antigen polymerase Wzy determines chain length regulation by WzzB and WzzpHS-2 in Shigella flexneri 2a.

PubMed

Carter, Javier A; Jiménez, Juan C; Zaldívar, Mercedes; Alvarez, Sergio A; Marolda, Cristina L; Valvano, Miguel A; Contreras, Inés

2009-10-01

The lipopolysaccharide O antigen of Shigella flexneri 2a has two preferred chain lengths, a short (S-OAg) composed of an average of 17 repeated units and a very long (VL-OAg) of about 90 repeated units. These chain length distributions are controlled by the chromosomally encoded WzzB and the plasmid-encoded Wzz(pHS-2) proteins, respectively. In this study, genes wzzB, wzz(pHS-2) and wzy (encoding the O-antigen polymerase) were cloned under the control of arabinose- and rhamnose-inducible promoters to investigate the effect of varying their relative expression levels on O antigen polysaccharide chain length distribution. Controlled expression of the chain length regulators wzzB and wzz(pHS-2) revealed a dose-dependent production of each modal length. Increase in one mode resulted in a parallel decrease in the other, indicating that chain length regulators compete to control the degree of O antigen polymerization. Also, when expression of the wzy gene is low, S-OAg but not VL-OAg is produced. Production of VL-OAg requires high induction levels of wzy. Thus, the level of expression of wzy is critical in determining O antigen modal distribution. Western blot analyses of membrane proteins showed comparable high levels of the WzzB and Wzz(pHS-2) proteins, but very low levels of Wzy. In vivo cross-linking experiments and immunoprecipitation of membrane proteins did not detect any direct interaction between Wzy and WzzB, suggesting the possibility that these two proteins may not interact physically but rather by other means such as via translocated O antigen precursors.

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.

In vitro fatty acid enrichment of macrophages alters inflammatory response and net cholesterol accumulation

PubMed Central

Wang, Shu; Wu, Dayong; Lamon-Fava, Stefania; Matthan, Nirupa R.; Honda, Kaori L.; Lichtenstein, Alice H.

2010-01-01

Dietary long-chain PUFA, both n-3 and n-6, have unique benefits with respect to CVD risk. The aim of the present study was to determine the mechanisms by which n-3 PUFA (EPA, DHA) and n-6 PUFA (linoleic acid (LA), arachidonic acid (AA)) relative to SFA (myristic acid (MA), palmitic acid (PA)) alter markers of inflammation and cholesterol accumulation in macrophages (MΦ). Cells treated with AA and EPA elicited significantly less inflammatory response than control cells or those treated with MA, PA and LA, with intermediate effects for DHA, as indicated by lower levels of mRNA and secretion of TNFα, IL-6 and monocyte chemoattractant protein-1. Differences in cholesterol accumulation after exposure to minimally modified LDL were modest. AA and EPA resulted in significantly lower MΦ scavenger receptor 1 mRNA levels relative to control or MA-, PA-, LA- and DHA-treated cells, and ATP-binding cassette A1 mRNA levels relative to control or MA-, PA- and LA-treated cells. These data suggest changes in the rate of bidirectional cellular cholesterol flux. In summary, individual long-chain PUFA have differential effects on inflammatory response and markers of cholesterol flux in MΦ which are not related to the n position of the first double bond, chain length or degree of saturation. PMID:19660150

Highly efficient and mild electrochemical mineralization of long-chain perfluorocarboxylic acids (C9-C10) by Ti/SnO2-Sb-Ce, Ti/SnO2-Sb/Ce-PbO2, and Ti/BDD electrodes.

PubMed

Lin, Hui; Niu, Junfeng; Xu, Jiale; Huang, Haiou; Li, Duo; Yue, Zhihan; Feng, Chenghong

2013-11-19

The electrochemical mineralization of environmentally persistent long-chain perfluorinated carboxylic acids (PFCAs), i.e., perfluorononanoic acid (C8F17COOH, PFNA) and perfluorodecanoic acid (C9F19COOH, PFDA) was investigated in aqueous solutions (0.25 mmol L(-1)) over Ti/SnO2-Sb-Ce (SnO2), Ti/SnO2-Sb/Ce-PbO2 (PbO2), and Ti/BDD (BDD) anodes under galvanostatic control at room temperature. Based on PFCA decay rate, total organic carbon (TOC) reduction, defluorination ratio, safety, and energy consumption, the performance of PbO2 electrode was comparable with that of BDD electrode. After 180 min electrolysis, the PFNA removals on BDD and PbO2 electrodes were 98.7 ± 0.4% and 97.1 ± 1.0%, respectively, while the corresponding PFDA removals were 96.0 ± 1.4% and 92.2 ± 1.9%. SnO2 electrode yielded lower PFCA removals and led to notable secondary pollution by Sb ions. The primary mineralization product, F(-), as well as trace amounts of intermediate PFCAs with shortened chain lengths, were detected in aqueous solution after electrolysis. On the basis of these results, a degradation mechanism including three potential routes is proposed: via formation of short-chain PFCAs by stepwise removal of CF2; direct mineralization to CO2 and HF; conversion to volatile fluorinated organic compounds. The results presented here demonstrate that electrochemical technique exhibits high efficiency in mineralizing PFNA and PFDA under mild conditions, and is promising for the treatment of long-chain PFCAs in wastewater.

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.

Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Diama, A.; Matthies, B.; Herwig, K. W.; Hansen, F. Y.; Criswell, L.; Mo, H.; Bai, M.; Taub, H.

2009-08-01

We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C24H50 denoted as C24) and dotriacontane (n-C32H66 denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 Å=√3 ag, where ag=2.46 Å is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by ˜10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

Structure and phase transitions of monolayers of intermediate-length n-alkanes on graphite studied by neutron diffraction and molecular dynamics simulation.

PubMed

Diama, A; Matthies, B; Herwig, K W; Hansen, F Y; Criswell, L; Mo, H; Bai, M; Taub, H

2009-08-28

We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C(24)H(50) denoted as C24) and dotriacontane (n-C(32)H(66) denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 A=sqrt[3a(g)], where a(g)=2.46 A is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a "smectic" phase in which the inter-row spacing within a lamella expands by approximately 10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

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.

From labdanes to drimanes. Degradation of the side chain of dihydrozamoranic acid.

PubMed

Rodilla, Jesús M L; Díez, D; Urones, J G; Rocha, Pedro M

2004-04-30

A new route for the degradation of the saturated side chain of dihydrozamoranic acid has been devised, giving an advanced intermediate, compound 14, useful for the synthesis of insect antifeedants such as warburganal and polygodial.

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.

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.

Evaluation of the Molecular Structural Parameters of Normal Rice Starch and Their Relationships with Its Thermal and Digestion Properties.

PubMed

Lin, Lingshang; Zhang, Qing; Zhang, Long; Wei, Cunxu

2017-09-12

The molecular structural parameters of six normal rice starches with different amylose contents were investigated through their iodine absorption spectra and gel permeation chromatography of fully branched and debranched starches. The thermal and digestion properties of starches were also determined and their relationships with molecular structural parameters were analyzed. Results showed that the molecular structural parameters of maximum absorption wavelength, blue value (BV), optical density 620 nm/550 nm (OD 620/550), amylose, intermediate component, and amylopectin, including its short branch-chains, long branch-chains, and branching degree, had high correlation in different determining methods. The intermediate component of starch was significantly positively related to amylose and negatively related to amylopectin, and the amylopectin branching degree was significantly positively related to amylopectin content and negatively related to amylose content. The gelatinization temperatures and enthalpy of native starch were significantly positively related to BV, OD 620/550, and amylose content and negatively related to amylopectin short branch-chains. The gelatinization temperatures and enthalpy of retrograded starch were significantly negatively related to amylopectin branching degree. The digestions of gelatinized and retrograded starches were significantly negatively related to the BV, OD 620/550, amylose, and intermediate component and positively related to amylopectin and its short branch-chains and branching degree.

Mechanism of insulin fibrillation: the structure of insulin under amyloidogenic conditions resembles a protein-folding intermediate.

PubMed

Hua, Qing-xin; Weiss, Michael A

2004-05-14

Insulin undergoes aggregation-coupled misfolding to form a cross-beta assembly. Such fibrillation has long complicated its manufacture and use in the therapy of diabetes mellitus. Of interest as a model for disease-associated amyloids, insulin fibrillation is proposed to occur via partial unfolding of a monomeric intermediate. Here, we describe the solution structure of human insulin under amyloidogenic conditions (pH 2.4 and 60 degrees C). Use of an enhanced sensitivity cryogenic probe at high magnetic field avoids onset of fibrillation during spectral acquisition. A novel partial fold is observed in which the N-terminal segments of the A- and B-chains detach from the core. Unfolding of the N-terminal alpha-helix of the A-chain exposes a hydrophobic surface formed by native-like packing of the remaining alpha-helices. The C-terminal segment of the B-chain, although not well ordered, remains tethered to this partial helical core. We propose that detachment of N-terminal segments makes possible aberrant protein-protein interactions in an amyloidogenic nucleus. Non-cooperative unfolding of the N-terminal A-chain alpha-helix resembles that observed in models of proinsulin folding intermediates and foreshadows the extensive alpha --> beta transition characteristic of mature fibrils.

Chain Assembly and Disassembly Processes Differently Affect the Conformational Space of Ubiquitin Chains.

PubMed

Kniss, Andreas; Schuetz, Denise; Kazemi, Sina; Pluska, Lukas; Spindler, Philipp E; Rogov, Vladimir V; Husnjak, Koraljka; Dikic, Ivan; Güntert, Peter; Sommer, Thomas; Prisner, Thomas F; Dötsch, Volker

2018-02-06

Ubiquitination is the most versatile posttranslational modification. The information is encoded by linkage type as well as chain length, which are translated by ubiquitin binding domains into specific signaling events. Chain topology determines the conformational space of a ubiquitin chain and adds an additional regulatory layer to this ubiquitin code. In particular, processes that modify chain length will be affected by chain conformations as they require access to the elongation or cleavage sites. We investigated conformational distributions in the context of chain elongation and disassembly using pulsed electron-electron double resonance spectroscopy in combination with molecular modeling. Analysis of the conformational space of diubiquitin revealed conformational selection or remodeling as mechanisms for chain recognition during elongation or hydrolysis, respectively. Chain elongation to tetraubiquitin increases the sampled conformational space, suggesting that a high intrinsic flexibility of K48-linked chains may contribute to efficient proteasomal degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Critical conditions of polymer adsorption and chromatography on non-porous substrates.

PubMed

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

2016-07-15

We present a novel thermodynamic theory and Monte Carlo simulation model for adsorption of macromolecules to solid surfaces that is applied for calculating the chain partition during separation on chromatographic columns packed with non-porous particles. We show that similarly to polymer separation on porous substrates, it is possible to attain three chromatographic modes: size exclusion chromatography at very weak or no adsorption, liquid adsorption chromatography when adsorption effects prevail, and liquid chromatography at critical conditions that occurs at the critical point of adsorption. The main attention is paid to the analysis of the critical conditions, at which the retention is chain length independent. The theoretical results are verified with specially designed experiments on isocratic separation of linear polystyrenes on a column packed with non-porous particles at various solvent compositions. Without invoking any adjustable parameters related to the column and particle geometry, we describe quantitatively the observed transition between the size exclusion and adsorption separation regimes upon the variation of solvent composition, with the intermediate mode occurring at a well-defined critical point of adsorption. A relationship is established between the experimental solvent composition and the effective adsorption potential used in model simulations. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure-Function Studies of Ser-289 in the Class C β-Lactamase from Enterobacter cloacae P99

PubMed Central

Trépanier, Sonia; Knox, James R.; Clairoux, Natalie; Sanschagrin, François; Levesque, Roger C.; Huletsky, Ann

1999-01-01

Site-directed mutagenesis of Ser-289 of the class C β-lactamase from Enterobacter cloacae P99 was performed to investigate the role of this residue in β-lactam hydrolysis. This amino acid lies near the active site of the enzyme, where it can interact with the C-3 substituent of cephalosporins. Kinetic analysis of six mutant β-lactamases with five cephalosporins showed that Ser-289 can be substituted by amino acids with nonpolar or polar uncharged side chains without altering the catalytic efficiency of the enzyme. These data suggest that Ser-289 is not essential in the binding or hydrolytic mechanism of AmpC β-lactamase. However, replacement by Lys or Arg decreased by two- to threefold the kcat of four of the five β-lactams tested, particularly cefoperazone, cephaloridine, and cephalothin. Three-dimensional models of the mutant β-lactamases revealed that the length and positive charge of the side chain of Lys and Arg could create an electrostatic linkage to the C-4 carboxylic acid group of the dihydrothiazine ring of the acyl intermediate which could slow the deacylation step or hinder release of the product. PMID:10049265

Inferring High-Confidence Human Protein-Protein Interactions

DTIC Science & Technology

2012-01-01

comprised proteins that had the same specific func- tion or were subunits of the same protein complex, such as branched chain keto acid E1 alpha (BCKDHA...and branched chain keto acid E1 beta (BCKDHB) [3,29], and dynein cytoplasmic 2 intermediate chain 1 (D2LIC) and dynein cytoplasmic 2 heavy chain 1...474.3 28.0 1337.0 BCKDHA 5 Branched chain keto acid dehydro. E1, alpha BCKDHB 4 Branched chain keto acid dehydro. E1, beta 4 471.4 29.0 1337.5 ARTN 2

The Small Subunit of Snapdragon Geranyl Diphosphate Synthase Modifies the Chain Length Specificity of Tobacco Geranylgeranyl Diphosphate Synthase in Planta[W

PubMed Central

Orlova, Irina; Nagegowda, Dinesh A.; Kish, Christine M.; Gutensohn, Michael; Maeda, Hiroshi; Varbanova, Marina; Fridman, Eyal; Yamaguchi, Shinjiro; Hanada, Atsushi; Kamiya, Yuji; Krichevsky, Alexander; Citovsky, Vitaly; Pichersky, Eran; Dudareva, Natalia

2009-01-01

Geranyl diphosphate (GPP), the precursor of many monoterpene end products, is synthesized in plastids by a condensation of dimethylallyl diphosphate and isopentenyl diphosphate (IPP) in a reaction catalyzed by homodimeric or heterodimeric GPP synthase (GPPS). In the heterodimeric enzymes, a noncatalytic small subunit (GPPS.SSU) determines the product specificity of the catalytic large subunit, which may be either an active geranylgeranyl diphosphate synthase (GGPPS) or an inactive GGPPS-like protein. Here, we show that expression of snapdragon (Antirrhinum majus) GPPS.SSU in tobacco (Nicotiana tabacum) plants increased the total GPPS activity and monoterpene emission from leaves and flowers, indicating that the introduced catalytically inactive GPPS.SSU found endogenous large subunit partner(s) and formed an active snapdragon/tobacco GPPS in planta. Bimolecular fluorescence complementation and in vitro enzyme analysis of individual and hybrid proteins revealed that two of four GGPPS-like candidates from tobacco EST databases encode bona fide GGPPS that can interact with snapdragon GPPS.SSU and form a functional GPPS enzyme in plastids. The formation of chimeric GPPS in transgenic plants also resulted in leaf chlorosis, increased light sensitivity, and dwarfism due to decreased levels of chlorophylls, carotenoids, and gibberellins. In addition, these transgenic plants had reduced levels of sesquiterpene emission, suggesting that the export of isoprenoid intermediates from the plastids into the cytosol was decreased. These results provide genetic evidence that GPPS.SSU modifies the chain length specificity of phylogenetically distant GGPPS and can modulate IPP flux distribution between GPP and GGPP synthesis in planta. PMID:20028839

A manifestation of the Ostwald step rule: molecular-dynamics simulations and free-energy landscape of the primary nucleation and melting of single-molecule polyethylene in dilute solution.

PubMed

Larini, L; Leporini, D

2005-10-08

The paper presents numerical results from extensive molecular-dynamics simulations of the crystallization process of a single polyethylene chain with N=500 monomers. The development of the ordered structure is seen to proceed along different routes involving either the global reorganization of the chain or, alternatively, well-separated connected nuclei. No dependence on the thermal history was observed at the late stages of the crystallization. The folding process involves several intermediate ordered metastable states, in strong analogy with the experiments, and ends up in a well-defined long-lived lamella with ten stems of approximately equal length, arranged into a regular, hexagonal pattern. This behavior may be seen as a microscopic manifestation of the Ostwald step rule. Both the metastable states and the long-lived one are evidenced as the local minima and the global one of the free-energy landscape, respectively. The study of the microscopic organization of the lamella evidenced that the two caps are rather flat, i.e., the loops connecting the stems are short. Interestingly, annealing the chain through the different metastable states leaves the average number of monomers per loop nearly unchanged. It is also seen that the chain ends, the so-called cilia, are localized on the surface of the lamella, in agreement with the experiments, and that structural fluctuations take place on the lamella surface, as noted by recent Monte Carlo simulations. The study of the melting process evidences that the degree of hysteresis is small.

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.

Critical temperatures and a critical chain length in saturated diacylphosphatidylcholines: calorimetric, ultrasonic and Monte Carlo simulation study of chain-melting/ordering in aqueous lipid dispersions.

PubMed

Kharakoz, Dmitry P; Panchelyuga, Maria S; Tiktopulo, Elizaveta I; Shlyapnikova, Elena A

2007-12-01

Chain-ordering/melting transition in a series of saturated diacylphosphatidylcholines (PCs) in aqueous dispersions have been studied experimentally (calorimetric and ultrasonic techniques) and theoretically (an Ising-like lattice model). The shape of the calorimetric curves was compared with the theoretical data and interpreted in terms of the lateral interactions and critical temperatures determined for each lipid studied. A critical chain length has been found (between 16 and 17 C-atoms per chain) which subdivides PCs into two classes with different phase behavior. In shorter lipids, the transition takes place above their critical temperatures meaning that this is an intrinsically continuous transition. In longer lipids, the transition occurs below the critical temperatures of the lipids, meaning that the transition is intrinsically discontinuous (first-order). This conclusion was supported independently by the ultrasonic relaxation sensitive to density fluctuations. Interestingly, it is this length that is the most abundant among the saturated chains in biological membranes.

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.

Understanding the factors affecting the activation of alkane by Cp′Rh(CO)2 (Cp′ = Cp or Cp*)

PubMed Central

George, Michael W.; Hall, Michael B.; Jina, Omar S.; Portius, Peter; Sun, Xue-Zhong; Towrie, Michael; Wu, Hong; Yang, Xinzheng; Zarić, Snežana D.

2010-01-01

Fast time-resolved infrared spectroscopic measurements have allowed precise determination of the rates of activation of alkanes by Cp′Rh(CO) (Cp′ = η5-C5H5 or η5-C5Me5). We have monitored the kinetics of C─H activation in solution at room temperature and determined how the change in rate of oxidative cleavage varies from methane to decane. The lifetime of CpRh(CO)(alkane) shows a nearly linear behavior with respect to the length of the alkane chain, whereas the related Cp*Rh(CO)(alkane) has clear oscillatory behavior upon changing the alkane. Coupled cluster and density functional theory calculations on these complexes, transition states, and intermediates provide the insight into the mechanism and barriers in order to develop a kinetic simulation of the experimental results. The observed behavior is a subtle interplay between the rates of activation and migration. Unexpectedly, the calculations predict that the most rapid process in these Cp′Rh(CO)(alkane) systems is the 1,3-migration along the alkane chain. The linear behavior in the observed lifetime of CpRh(CO)(alkane) results from a mechanism in which the next most rapid process is the activation of primary C─H bonds (─CH3 groups), while the third key step in this system is 1,2-migration with a slightly slower rate. The oscillatory behavior in the lifetime of Cp*Rh(CO)(alkane) with respect to the alkane’s chain length follows from subtle interplay between more rapid migrations and less rapid primary C─H activation, with respect to CpRh(CO)(alkane), especially when the CH3 group is near a gauche turn. This interplay results in the activation being controlled by the percentage of alkane conformers. PMID:21048088

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.

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.

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.

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.

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

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.

Theoretical Studies of Relaxation and Optical Properties of Polymers

NASA Astrophysics Data System (ADS)

Jin, Bih-Yaw

1993-01-01

This thesis is composed of two parts. In the part one, the empirical correlation between the logarithm of tunneling splittings and the temperature at which the spin-lattice relaxation time is minimum for methyl groups in different molecular crystals is explained successfully by taking multiphonon processes into account. We show that one phonon transitions dominate in the low barrier limit. However, in the intermediate barrier range and high barrier limit, it is necessary to include multiphonon processes. We also show that the empirical correlation depends only logarithmically on the details of the phonon bath. In the part two, we have investigated the optical and relaxation properties of conjugated polymers. The connection between the vibronic picture of Raman scattering and the third order perturbation approach in solid state physics is clarified in chapter 2. Starting from the Kramers -Heissenberg-Dirac formula for Raman scattering, we derive expressions for the Condon and Herzberg-Teller terms from a simple two-level system to a two-band system, i.e. polyacetylene, by using traditional vibronic picture. Both the Condon and Herzberg-Teller terms contribute to two-band processes, while three-band processes consist only of Herzberg-Teller terms in the solid state limit. Close to resonance the Condon term dominates and converges to the usual solid state result. In the off-resonance region the Herzberg -Teller term is comparable to Condon term for both small molecule and solid state system. In chapter 3, we will concentrate on the lattice relaxation of the lowest optically allowed 1B_ {u} state, especially, the effect of electron correlation on the excited state geometric relaxation for finite polyenes. We have examined the competition between electron-electron interaction and electron-phonon coupling on the formation of localized lattice distortion in the 1B_{u} state for finite polyene with chain length up to 30 double bonds. The chain length dependence of the lattice relaxation in 1B _{u} state has been studied thoroughly within singly excited configuration interaction for short range Hubbard, extended Hubbard model and long-range Pariser -Parr-Pople model. We have found that local distortion is not favored until a critical chain length is reached. Beyond this critical length, which is a function of electron-electron interaction and electron-phonon coupling strength, a self -trapped exciton is formed rather than the separated soliton -antisoliton configuration as expected in the independent electron theory. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617 -253-5668; Fax 617-253-1690.).

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.

Understanding the length dependence of molecular junction thermopower.

PubMed

Karlström, Olov; Strange, Mikkel; Solomon, Gemma C

2014-01-28

Thermopower of molecular junctions is sensitive to details in the junction and may increase, decrease, or saturate with increasing chain length, depending on the system. Using McConnell's theory for exponentially suppressed transport together with a simple and easily interpretable tight binding model, we show how these different behaviors depend on the molecular backbone and its binding to the contacts. We distinguish between resonances from binding groups or undercoordinated electrode atoms, and those from the periodic backbone. It is demonstrated that while the former gives a length-independent contribution to the thermopower, possibly changing its sign, the latter determines its length dependence. This means that the question of which orbitals from the periodic chain that dominate the transport should not be inferred from the sign of the thermopower but from its length dependence. We find that the same molecular backbone can, in principle, show four qualitatively different thermopower trends depending on the binding group: It can be positive or negative for short chains, and it can either increase or decrease with length.

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.

Molecular cloning and characterization of two mouse peroxisome proliferator-activated receptor alpha (PPARalpha)-regulated peroxisomal acyl-CoA thioesterases.

PubMed

Westin, Maria A K; Alexson, Stefan E H; Hunt, Mary C

2004-05-21

Peroxisomes are organelles that function in the beta-oxidation of long- and very long-chain acyl-CoAs, bile acid-CoA intermediates, prostaglandins, leukotrienes, thromboxanes, dicarboxylic fatty acids, pristanic acid, and xenobiotic carboxylic acids. The very long- and long-chain acyl-CoAs are mainly chain-shortened and then transported to mitochondria for further metabolism. We have now identified and characterized two peroxisomal acyl-CoA thioesterases, named PTE-Ia and PTE-Ic, that hydrolyze acyl-CoAs to the free fatty acid and coenzyme A. PTE-Ia and PTE-Ic show 82% sequence identity at the amino acid level, and a putative peroxisomal type 1 targeting signal of -AKL was identified at the carboxyl-terminal end of both proteins. Localization experiments using green fluorescent fusion protein showed PTE-Ia and PTE-Ic to be localized in peroxisomes. Despite their high level of sequence identity, we show that PTE-Ia is mainly active on long-chain acyl-CoAs, whereas PTE-Ic is mainly active on medium-chain acyl-CoAs. Lack of regulation of enzyme activity by free CoASH suggests that PTE-Ia and PTE-Ic regulate intraperoxisomal levels of acyl-CoA, and they may have a function in termination of beta-oxidation of fatty acids of different chain lengths. Tissue expression studies revealed that PTE-Ia is highly expressed in kidney, whereas PTE-Ic is most highly expressed in spleen, brain, testis, and proximal and distal intestine. Both PTE-Ia and PTE-Ic were highly up-regulated in mouse liver by treatment with the peroxisome proliferator WY-14,643 and by fasting in a peroxisome proliferator-activated receptor alpha-dependent manner. These data show that PTE-Ia and PTE-Ic have different functions based on different substrate specificities and tissue expression.

Substrate Trapping in Crystals of the Thiolase OleA Identifies Three Channels That Enable Long Chain Olefin Biosynthesis.

PubMed

Goblirsch, Brandon R; Jensen, Matthew R; Mohamed, Fatuma A; Wackett, Lawrence P; Wilmot, Carrie M

2016-12-23

Phylogenetically diverse microbes that produce long chain, olefinic hydrocarbons have received much attention as possible sources of renewable energy biocatalysts. One enzyme that is critical for this process is OleA, a thiolase superfamily enzyme that condenses two fatty acyl-CoA substrates to produce a β-ketoacid product and initiates the biosynthesis of long chain olefins in bacteria. Thiolases typically utilize a ping-pong mechanism centered on an active site cysteine residue. Reaction with the first substrate produces a covalent cysteine-thioester tethered acyl group that is transferred to the second substrate through formation of a carbon-carbon bond. Although the basics of thiolase chemistry are precedented, the mechanism by which OleA accommodates two substrates with extended carbon chains and a coenzyme moiety-unusual for a thiolase-are unknown. Gaining insights into this process could enable manipulation of the system for large scale olefin production with hydrocarbon chains lengths equivalent to those of fossil fuels. In this study, mutagenesis of the active site cysteine in Xanthomonas campestris OleA (Cys 143 ) enabled trapping of two catalytically relevant species in crystals. In the resulting structures, long chain alkyl groups (C 12 and C 14 ) and phosphopantetheinate define three substrate channels in a T-shaped configuration, explaining how OleA coordinates its two substrates and product. The C143A OleA co-crystal structure possesses a single bound acyl-CoA representing the Michaelis complex with the first substrate, whereas the C143S co-crystal structure contains both acyl-CoA and fatty acid, defining how a second substrate binds to the acyl-enzyme intermediate. An active site glutamate (Gluβ 117 ) is positioned to deprotonate bound acyl-CoA and initiate carbon-carbon bond formation. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

N-substituted imidazolines and ethylenediamines and their action on alpha- and beta-adrenergic receptors.

PubMed

Hamada, A; Yaden, E L; Horng, J S; Ruffolo, R R; Patil, P N; Miller, D D

1985-09-01

A series of N-substituted imidazolines and ethylenediamines were synthesized and examined for their activity in alpha- and beta-adrenergic systems. The length of the intermediate side chain between the catechol and imidazoline ring or the amine of the ethylenediamine segment was shown to affect the adrenergic activity. N-[2-(3,4-Dihydroxyphenyl)ethyl]imidazoline hydrochloride (2) and N-[2-(3,4-dihydroxyphenyl)ethyl]ethylenediamine dihydrochloride (4), both with two methylene groups between the catechol and amine segment, were found to be somewhat selective for alpha 2-adrenergic receptors while 1-(3,4-dihydroxybenzyl)imidazoline hydrochloride (1) and N-2-(3,4-dihydroxybenzyl)ethylenediamine dihydrochloride (3), both with one methylene group between the catechol and amine segment, were more selective for alpha1-adrenergic receptors in a pithed rat model. Of the four compounds examined, only compound 2 showed significant direct activity on beta1- and beta2-adrenergic receptors.

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.

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

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.

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.

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.

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

Density- and trait-mediated effects of a parasite and a predator in a tri-trophic food web

PubMed Central

Banerji, Aabir; Duncan, Alison B; Griffin, Joanne S; Humphries, Stuart; Petchey, Owen L; Kaltz, Oliver

2015-01-01

1. Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density or trait mediated. 2. We studied a tri-trophic food chain comprised of (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum) and (iv) a parasite of the intermediate consumer (Holospora undulata). A fully factorial experimental manipulation of predator and parasite presence/absence was combined with analyses of population dynamics, modelling and analyses of host (Paramecium) morphology and behaviour. 3. Predation and parasitism each reduced the abundance of the intermediate consumer (Paramecium), and parasitism indirectly reduced the abundance of the basal resource (Serratia). However, in combination, predation and parasitism had non-additive effects on the abundance of the intermediate consumer, as well as on that of the basal resource. In both cases, the negative effect of parasitism seemed to be effaced by predation. 4. Infection of the intermediate consumer reduced predator abundance. Modelling and additional experimentation revealed that this was most likely due to parasite reduction of intermediate host abundance (a density-mediated effect), as opposed to changes in predator functional or numerical response. 5. Parasitism altered morphological and behavioural traits, by reducing host cell length and increasing the swimming speed of cells with moderate parasite loads. Additional tests showed no significant difference in Didinium feeding rate on infected and uninfected hosts, suggesting that the combination of these modifications does not affect host vulnerability to predation. However, estimated rates of encounter with Serratia based on these modifications were higher for infected Paramecium than for uninfected Paramecium. 6. A mixture of density-mediated and trait-mediated indirect effects of parasitism on non-host species creates rich and complex possibilities for effects of parasites in food webs that should be included in assessments of possible impacts of parasite eradication or introduction. PMID:25382389

Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini.

PubMed Central

Lim, S K; Maquat, L E

1992-01-01

Previous studies have demonstrated that nonsense codons within beta zero-thalassemic or in vitro-mutagenized human beta-globin transgenes result in the production of mRNAs that are degraded abnormally rapidly in the cytoplasm of murine erythroid cells. As a consequence, three RNA degradative intermediates are formed that lack sequences from either exon I or exons I and II. We show here that the intermediates, like the full-length mRNA from which they derive and the endogenous murine beta maj-globin mRNA, bind to the anticap monoclonal antibody H-20 in a way that is competed by the cap analogue m7G and eliminated by prior exposure to tobacco acid pyrophosphatase. Furthermore, the intermediates, like the two full-length mRNAs, are resistant to a 5'----3' exonuclease activity isolated from HeLa cell nuclei that degrades uncapped but not capped ribopolymers. Based on these observations, the intermediates appear to possess a structure that is indistinguishable from the cap at the 5' end of mRNA, i.e. a methylated nucleoside that is linked to the RNA by a 5'-5' phosphodiester bond. Detection of the intermediates during murine development was concomitant with detection of full-length thalassemic mRNA. Intermediate production appears to be influenced by RNA structure as indicated by the products that derive from a beta zero-thalassemic beta-globin transgene harboring a structural alteration (a 4 bp deletion) that was larger than any of those previously studied. Images PMID:1324170

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.

ATXN2 with intermediate-length CAG/CAA repeats does not seem to be a risk factor in hereditary spastic paraplegia.

PubMed

Nielsen, Troels Tolstrup; Svenstrup, Kirsten; Budtz-Jørgensen, Esben; Eiberg, Hans; Hasholt, Lis; Nielsen, Jørgen E

2012-10-15

Hereditary spastic paraplegia (HSP) confines a group of heterogeneous neurodegenerative disorders characterized by progressive spasticity and lower limb weakness. Age of onset is highly variable even in familial cases with known mutations suggesting that the disease is modulated by other yet unknown parameters. Although progressive gait disturbances, lower limb spasticity and extensor plantar responses are hallmarks of HSP these characteristics are also found in other neurodegenerative disorders, e.g. amytrophic lateral sclerosis (ALS). HSP has been linked to ALS and frontotemporal degeneration with motor neuron disease (FTD-MND), since TDP-43 positive inclusions have recently been found in an HSP subtype, and TDP-43 are found in abundance in pathological inclusions of both ALS and FTD-MND. Furthermore, ataxin-2 (encoded by the gene ATXN2), a polyglutamine containing protein elongated in spinocerebellar ataxia type 2, has been shown to be a modulator of TDP-43 induced toxicity in ALS animal and cell models. Finally, it has been shown that ATXN2 with non-pathogenic intermediate-length CAG/CAA repeat elongations (encoding the polyglutamine tract) is a genetic risk factor of ALS. Considering the similarities in the disease phenotype and the neuropathological link between ALS and HSP we hypothesized that intermediate-length CAG/CAA repeats in ATXN2 could be a modulator of HSP. We show that in a cohort of 181 HSP patients 4.9 % of the patients had intermediate-length CAG/CAA repeats in ATXN2 which was not significantly different from the frequencies in a Danish control cohort or in American and European control populations. However, the mean age of onset was significantly lower in HSP patients with intermediate-length CAG/CAA repeats in ATXN2 compared to patients with normal length repeats. Based on these results we conclude that ATXN2 is most likely not a risk factor of HSP, whereas it might serve as a modulator of age of onset. Copyright © 2012 Elsevier B.V. All rights reserved.

Toxoplasma gondii: isolation, biological and molecular characterisation of samples from free-range Gallus gallus domesticus from countryside Southeast Brazil.

PubMed

Ferreira, Tamiris Cristine Ribeiro; Buery, Julyana Cerqueira; Moreira, Narcisa Imaculada Brant; Santos, Claudiney Biral; Costa, Júlia Gatti Ladeia; Pinto, Lorena Velozo; Baraviera, Ramon Castro de Araújo; Vitor, Ricardo Wagner Almeida; Fux, Blima

2018-05-24

Toxoplasma gondii presents a high prevalence worldwide, infecting several animals. Felines are considered the definitive hosts and among the intermediate hosts we highlight mammals and birds. The man can become infected by ingesting tissue cysts present in birds and mammals. Biological and molecular aspects of T. gondii allows a better understanding of the epidemiology of toxoplasmosis. This work is a serologic screening of 58 chickens grown (Gallus gallus domesticus) for human consumption in Espírito Santo State, by means of indirect haemagglutination assay (IHA). Thirteen chickens tested positive for anti-T. gondii antibodies. The heart and brain of five positive chickens were harvested, treated with pepsin and inoculated separately, in two Swiss mice, intraperitoneally. Tachyzoites were observed in the peritoneum of all the animals, between seven and 10 days after the inoculum. Ten isolates were obtained and biologically characterised in BALB/c mice inoculated with 101 to 104 tachyzoites. All isolates were classified as virulent or intermediately virulent. Isolates were genotyped by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, revealing three different genotypes. None of the isolates exhibited the clonal type I, II or III genotype. No genotypic differences were observed between the isolates from the brain or heart from the same bird.

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.

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.

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...

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.

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

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

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.

A residue located at the junction of the head and stalk regions of measles virus fusion protein regulates membrane fusion by controlling conformational stability.

PubMed

Satoh, Yuto; Yonemori, Saeka; Hirose, Mitsuhiro; Shogaki, Hiroko; Wakimoto, Hiroshi; Kitagawa, Yoshinori; Gotoh, Bin; Shirai, Tsuyoshi; Takahashi, Ken-Ichi; Itoh, Masae

2017-02-01

The fusion (F) protein of measles virus performs refolding from the thermodynamically metastable prefusion form to the highly stable postfusion form via an activated unstable intermediate stage, to induce membrane fusion. Some amino acids involved in the fusion regulation cluster in the heptad repeat B (HR-B) domain of the stalk region, among which substitution of residue 465 by various amino acids revealed that fusion activity correlates well with its side chain length from the Cα (P<0.01) and van der Waals volume (P<0.001), except for Phe, Tyr, Trp, Pro and His carrying ring structures. Directed towards the head region, longer side chains of the non-ring-type 465 residues penetrate more deeply into the head region and may disturb the hydrophobic interaction between the stalk and head regions and cause destabilization of the molecule by lowering the energy barrier for refolding, which conferred the F protein enhanced fusion activity. Contrarily, the side chain of ring-type 465 residues turned away from the head region, resulting in not only no contact with the head region but also extensive coverage of the HR-B surface, which may prevent the dissociation of the HR-B bundle for initiation of membrane fusion and suppress fusion activity. Located in the HR-B domain just at the junction between the head and stalk regions, amino acid 465 is endowed with a possible ability to either destabilize or stabilize the F protein depending on its molecular volume and the direction of the side chain, regulating fusion activity of measles virus F protein.

Zee electrical interconnect

NASA Technical Reports Server (NTRS)

Rust, Thomas M. (Inventor); Gaddy, Edward M. (Inventor); Herriage, Michael J. (Inventor); Patterson, Robert E. (Inventor); Partin, Richard D. (Inventor)

2001-01-01

An interconnect, having some length, that reliably connects two conductors separated by the length of the interconnect when the connection is made but in which one length if unstressed would change relative to the other in operation. The interconnect comprises a base element an intermediate element and a top element. Each element is rectangular and formed of a conducting material and has opposed ends. The elements are arranged in a generally Z-shape with the base element having one end adapted to be connected to one conductor. The top element has one end adapted to be connected to another conductor and the intermediate element has its ends disposed against the other end of the base and the top element. Brazes mechanically and electrically interconnect the intermediate element to the base and the top elements proximate the corresponding ends of the elements. When the respective ends of the base and the top elements are connected to the conductors, an electrical connection is formed therebetween, and when the conductors are relatively moved or the interconnect elements change length the elements accommodate the changes and the associated compression and tension forces in such a way that the interconnect does not mechanically fatigue.

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

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

Exploring Indirect Sources of Human Exposure to Perfluoroalkyl Carboxylates (PFCAs): Evaluating Uptake, Elimination, and Biotransformation of Polyfluoroalkyl Phosphate Esters (PAPs) in the Rat

PubMed Central

D’eon, Jessica C.; Mabury, Scott A.

2011-01-01

Background Perfluorinated carboxylic acids (PFCAs) are ubiquitous in human sera worldwide. Biotransformation of the polyfluoroalkyl phosphate esters (PAPs) is a possible source of PFCA exposure, because PAPs are used in food-contact paper packaging and have been observed in human sera. Objectives We determined pharmacokinetic parameters for the PAP monoesters (monoPAPs) and PAP diesters (diPAPs), as well as biotransformation yields to the PFCAs, using a rat model. Methods The animals were dosed intravenously or by oral gavage with a mixture of 4:2, 6:2, 8:2, and 10:2 monoPAP or diPAP chain lengths. Concentrations of the PAPs and PFCAs, as well as metabolic intermediates and phase II metabolites, were monitored over time in blood, urine, and feces. Results The diPAPs were bioavailable, with bioavailability decreasing as the chain length increased from 4 to 10 perfluorinated carbons. The monoPAPs were not absorbed from the gut; however, we found evidence to suggest phosphate-ester cleavage within the gut contents. We observed biotransformation to the PFCAs for both monoPAP and diPAP congeners. Conclusions Using experimentally derived biotransformation yields, perfluorooctanoic acid (PFOA) sera concentrations were predicted from the biotransformation of 8:2 diPAP at concentrations observed in human serum. Because of the long human serum half-life of PFOA, biotransformation of diPAP even with low-level exposure could over time result in significant exposure to PFOA. Although humans are exposed directly to PFCAs in food and dust, the pharmacokinetic parameters determined here suggest that PAP exposure should be considered a significant indirect source of human PFCA contamination. PMID:21059488

Thermal and structural behavior of anhydrous milk fat. 3. Influence of cooling rate.

PubMed

Lopez, C; Lesieur, P; Bourgaux, C; Ollivon, M

2005-02-01

The crystallization behavior of anhydrous milk fat has been examined with a new instrument coupling time-resolved synchrotron x-ray diffraction as a function of temperature (XRDT) at both small and wide angles and high-sensitivity differential scanning calorimetry. Crystallizations were monitored at cooling rates of 3 and 1 degrees C/ min from 60 to -10 degrees C to determine the triacylglycerol organizations formed. Simultaneous thermal analysis permitted the correlation of the formation/melting of the different crystalline species monitored by XRDT to the thermal events recorded by differential scanning calorimetry. At intermediate cooling rates, milk fat triacylglycerols sequentially crystallize in 3 different lamellar structures with double-chain length of 46 and 38.5 A and a triple-chain length of 72 A stackings of alpha type, which are correlated to 2 exothermic peaks at 17.2 and 13.7 degrees C, respectively. A time-dependent slow sub-alpha <--> alpha reversible transition is observed at -10 degrees C. Subsequent heating at 2 degrees C/min has shown numerous structural rearrangements of the alpha varieties into a single beta' form before final melting. This polymorphic evolution on heating, as well as the final melting point observed (approximately 39 degrees C), confirmed that cooling at 3 degrees C/min leads to the formation of crystalline varieties that are not at equilibrium. An overall comparison of the thermal and structural properties of the crystalline species formed as a function of the cooling rate and stabilization time is presented. The influence on crystal size of the cooling rates applied in situ using temperature-controlled polarized microscopy is also determined for comparison.

Dual influences of ecosystem size and disturbance on food chain length in streams.

PubMed

McHugh, Peter A; McIntosh, Angus R; Jellyman, Phillip G

2010-07-01

The number of trophic transfers occurring between basal resources and top predators, food chain length (FCL), varies widely in the world's ecosystems for reasons that are poorly understood, particularly for stream ecosystems. Available evidence indicates that FCL is set by energetic constraints, environmental stochasticity, or ecosystem size effects, although no single explanation has yet accounted for FCL patterns in a broad sense. Further, whether environmental disturbance can influence FCL has been debated on both theoretical and empirical grounds for quite some time. Using data from sixteen South Island, New Zealand streams, we determined whether the so-called ecosystem size, disturbance, or resource availability hypotheses could account for FCL variation in high country fluvial environments. Stable isotope-based estimates of maximum trophic position ranged from 2.6 to 4.2 and averaged 3.5, a value on par with the global FCL average for streams. Model-selection results indicated that stream size and disturbance regime best explained across-site patterns in FCL, although resource availability was negatively correlated with our measure of disturbance; FCL approached its maximum in large, stable springs and was <3.5 trophic levels in small, fishless and/or disturbed streams. Community data indicate that size influenced FCL, primarily through its influence on local fish species richness (i.e., via trophic level additions and/or insertions), whereas disturbance did so via an effect on the relative availability of intermediate predators (i.e., predatory invertebrates) as prey for fishes. Overall, our results demonstrate that disturbance can have an important food web-structuring role in stream ecosystems, and further imply that pluralistic explanations are needed to fully understand the range of structural variation observed for real food webs.

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.

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.

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.

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.

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.

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.

Topology of polymer chains under nanoscale confinement.

PubMed

Satarifard, Vahid; Heidari, Maziar; Mashaghi, Samaneh; Tans, Sander J; Ejtehadi, Mohammad Reza; Mashaghi, Alireza

2017-08-24

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of l p under a spherical confinement of radius R c . At low values of l p /R c , the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high l p /R c , the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of l p /R c , at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross topologies have nearly the same contact orders. Such degeneracy implies that the kinetics and transition rates between the topological states cannot be solely explained by contact order. We expect these findings to be of general importance in understanding chaperone assisted protein folding, chromosome architecture, and the evolution of molecular folds.

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.

Arabidopsis and Maize RidA Proteins Preempt Reactive Enamine/Imine Damage to Branched-Chain Amino Acid Biosynthesis in Plastids[C][W][OPEN

PubMed Central

Niehaus, Thomas D.; Nguyen, Thuy N.D.; Gidda, Satinder K.; ElBadawi-Sidhu, Mona; Lambrecht, Jennifer A.; McCarty, Donald R.; Downs, Diana M.; Cooper, Arthur J.L.; Fiehn, Oliver; Mullen, Robert T.; Hanson, Andrew D.

2014-01-01

RidA (for Reactive Intermediate Deaminase A) proteins are ubiquitous, yet their function in eukaryotes is unclear. It is known that deleting Salmonella enterica ridA causes Ser sensitivity and that S. enterica RidA and its homologs from other organisms hydrolyze the enamine/imine intermediates that Thr dehydratase forms from Ser or Thr. In S. enterica, the Ser-derived enamine/imine inactivates a branched-chain aminotransferase; RidA prevents this damage. Arabidopsis thaliana and maize (Zea mays) have a RidA homolog that is predicted to be plastidial. Expression of either homolog complemented the Ser sensitivity of the S. enterica ridA mutant. The purified proteins hydrolyzed the enamines/imines formed by Thr dehydratase from Ser or Thr and protected the Arabidopsis plastidial branched-chain aminotransferase BCAT3 from inactivation by the Ser-derived enamine/imine. In vitro chloroplast import assays and in vivo localization of green fluorescent protein fusions showed that Arabidopsis RidA and Thr dehydratase are chloroplast targeted. Disrupting Arabidopsis RidA reduced root growth and raised the root and shoot levels of the branched-chain amino acid biosynthesis intermediate 2-oxobutanoate; Ser treatment exacerbated these effects in roots. Supplying Ile reversed the root growth defect. These results indicate that plastidial RidA proteins can preempt damage to BCAT3 and Ile biosynthesis by hydrolyzing the Ser-derived enamine/imine product of Thr dehydratase. PMID:25070638

Dual mechanism of brain injury and novel treatment strategy in maple syrup urine disease.

PubMed

Zinnanti, William J; Lazovic, Jelena; Griffin, Kathleen; Skvorak, Kristen J; Paul, Harbhajan S; Homanics, Gregg E; Bewley, Maria C; Cheng, Keith C; Lanoue, Kathryn F; Flanagan, John M

2009-04-01

Maple syrup urine disease (MSUD) is an inherited disorder of branched-chain amino acid metabolism presenting with life-threatening cerebral oedema and dysmyelination in affected individuals. Treatment requires life-long dietary restriction and monitoring of branched-chain amino acids to avoid brain injury. Despite careful management, children commonly suffer metabolic decompensation in the context of catabolic stress associated with non-specific illness. The mechanisms underlying this decompensation and brain injury are poorly understood. Using recently developed mouse models of classic and intermediate maple syrup urine disease, we assessed biochemical, behavioural and neuropathological changes that occurred during encephalopathy in these mice. Here, we show that rapid brain leucine accumulation displaces other essential amino acids resulting in neurotransmitter depletion and disruption of normal brain growth and development. A novel approach of administering norleucine to heterozygous mothers of classic maple syrup urine disease pups reduced branched-chain amino acid accumulation in milk as well as blood and brain of these pups to enhance survival. Similarly, norleucine substantially delayed encephalopathy in intermediate maple syrup urine disease mice placed on a high protein diet that mimics the catabolic stress shown to cause encephalopathy in human maple syrup urine disease. Current findings suggest two converging mechanisms of brain injury in maple syrup urine disease including: (i) neurotransmitter deficiencies and growth restriction associated with branched-chain amino acid accumulation and (ii) energy deprivation through Krebs cycle disruption associated with branched-chain ketoacid accumulation. Both classic and intermediate models appear to be useful to study the mechanism of brain injury and potential treatment strategies for maple syrup urine disease. Norleucine should be further tested as a potential treatment to prevent encephalopathy in children with maple syrup urine disease during catabolic stress.

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.

Web Supplement to "Teaching Chain-Weight Real GDP Measures."

ERIC Educational Resources Information Center

Cahill, Miles B.

2003-01-01

Describes a Web site that is a companion to the Miles Cahill article, "Teaching Chain-Weight Real GDP Measures." States that the exercises are useful because intermediate level textbooks treat this topic casually. Indicates that the Web site contains the comment tool, an overview of the concepts, and links to article references. (JEH)

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.

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.

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.

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.

ATXN2 trinucleotide repeat length correlates with risk of ALS.

PubMed

Sproviero, William; Shatunov, Aleksey; Stahl, Daniel; Shoai, Maryam; van Rheenen, Wouter; Jones, Ashley R; Al-Sarraj, Safa; Andersen, Peter M; Bonini, Nancy M; Conforti, Francesca L; Van Damme, Philip; Daoud, Hussein; Del Mar Amador, Maria; Fogh, Isabella; Forzan, Monica; Gaastra, Ben; Gellera, Cinzia; Gitler, Aaron D; Hardy, John; Fratta, Pietro; La Bella, Vincenzo; Le Ber, Isabelle; Van Langenhove, Tim; Lattante, Serena; Lee, Yi-Chung; Malaspina, Andrea; Meininger, Vincent; Millecamps, Stéphanie; Orrell, Richard; Rademakers, Rosa; Robberecht, Wim; Rouleau, Guy; Ross, Owen A; Salachas, Francois; Sidle, Katie; Smith, Bradley N; Soong, Bing-Wen; Sorarù, Gianni; Stevanin, Giovanni; Kabashi, Edor; Troakes, Claire; van Broeckhoven, Christine; Veldink, Jan H; van den Berg, Leonard H; Shaw, Christopher E; Powell, John F; Al-Chalabi, Ammar

2017-03-01

We investigated a CAG trinucleotide repeat expansion in the ATXN2 gene in amyotrophic lateral sclerosis (ALS). Two new case-control studies, a British dataset of 1474 ALS cases and 567 controls, and a Dutch dataset of 1328 ALS cases and 691 controls were analyzed. In addition, to increase power, we systematically searched PubMed for case-control studies published after 1 August 2010 that investigated the association between ATXN2 intermediate repeats and ALS. We conducted a meta-analysis of the new and existing studies for the relative risks of ATXN2 intermediate repeat alleles of between 24 and 34 CAG trinucleotide repeats and ALS. There was an overall increased risk of ALS for those carrying intermediate sized trinucleotide repeat alleles (odds ratio 3.06 [95% confidence interval 2.37-3.94]; p = 6 × 10 -18 ), with an exponential relationship between repeat length and ALS risk for alleles of 29-32 repeats (R 2  = 0.91, p = 0.0002). No relationship was seen for repeat length and age of onset or survival. In contrast to trinucleotide repeat diseases, intermediate ATXN2 trinucleotide repeat expansion in ALS does not predict age of onset but does predict disease risk. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

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.

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).

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.

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

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.

Organic intermediates in the anaerobic biodegradation of coal to methane under laboratory conditions

USGS Publications Warehouse

Orem, William H.; Voytek, Mary A.; Jones, Elizabeth J.; Lerch, Harry E.; Bates, Anne L.; Corum, Margo D.; Warwick, Peter D.; Clark, Arthur C.

2010-01-01

Organic intermediates in coal fluids produced by anaerobic biodegradation of geopolymers in coal play a key role in the production of methane in natural gas reservoirs. Laboratory biodegradation experiments on sub-bituminous coal from Texas, USA, were conducted using bioreactors to examine the organic intermediates relevant to methane production. Production of methane in the bioreactors was linked to acetate accumulation in bioreactor fluid. Long chain fatty acids, alkanes (C19–C36) and various low molecular weight aromatics, including phenols, also accumulated in the bioreactor fluid and appear to be the primary intermediates in the biodegradation pathway from coal-derived geopolymers to acetate and methane.

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.

Static pile load tests on driven piles into Intermediate-Geo Materials.

DOT National Transportation Integrated Search

2016-09-01

The Wisconsin Department of Transportation (WisDOT) has concerns with both predicting pile lengths and pile capacities for H-piles driven into Intermediate-Geo Materials (IGM). The goal of the research was to perform 7 static axial load tests at 7 lo...

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.

Thermodynamic perturbation theory for fused sphere hard chain fluids using nonadditive interactions

NASA Astrophysics Data System (ADS)

Abu-Sharkh, Basel F.; Sunaidi, Abdallah; Hamad, Esam Z.

2004-03-01

A model is developed for the equation of state of fused chains based on Wertheim thermodynamic perturbation theory and nonadditive size interactions. The model also assumes that the structure (represented by the radial distribution function) of the fused chain fluid is the same as that of the touching hard sphere chain fluid. The model is completely based on spherical additive and nonadditive size interactions. The model has the advantage of offering good agreement with simulation data while at the same time being independent of fitted parameters. The model is most accurate for short chains, small values of Δ (slightly fused spheres) and at intermediate (liquidlike) densities.

Folding thermodynamics of pseudoknotted chain conformations

PubMed Central

Kopeikin, Zoia; Chen, Shi-Jie

2008-01-01

We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions. PMID:16674261

Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

PubMed Central

Serwer, Philip; Wright, Elena T.

2012-01-01

We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

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...

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.

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.

Features of the Phosphatidylinositol Cycle and its Role in Signal Transduction.

PubMed

Epand, Richard M

2017-08-01

The phosphatidylinositol cycle (PI-cycle) has a central role in cell signaling. It is the major pathway for the synthesis of phosphatidylinositol and its phosphorylated forms. In addition, some lipid intermediates of the PI-cycle, including diacylglycerol and phosphatidic acid, are also important lipid signaling agents. The PI-cycle has some features that are important for the understanding of its role in the cell. As a cycle, the intermediates will be regenerated. The PI-cycle requires a large amount of metabolic energy. There are different steps of the cycle that occur in two different membranes, the plasma membrane and the endoplasmic reticulum. In order to complete the PI-cycle lipid must be transferred between the two membranes. The role of the Nir proteins in the process has recently been elucidated. The lipid intermediates of the PI-cycle are normally highly enriched with 1-stearoyl-2-arachidonoyl molecular species in mammals. This enrichment will be retained as long as the intermediates are segregated from other lipids of the cell. However, there is a significant fraction (>15 %) of lipids in the PI-cycle of normal cells that have other acyl chains. Phosphatidylinositol largely devoid of arachidonoyl chains are found in cancer cells. Phosphatidylinositol species with less unsaturation will not be as readily converted to phosphatidylinositol-3,4,5-trisphosphate, the lipid required for the activation of Akt with resulting effects on cell proliferation. Thus, the cyclical nature of the PI-cycle, its dependence on acyl chain composition and its requirement for lipid transfer between two membranes, explain many of the biological properties of this cycle.

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.

Primitive-path statistics of entangled polymers: mapping multi-chain simulations onto single-chain mean-field models

NASA Astrophysics Data System (ADS)

Steenbakkers, Rudi J. A.; Tzoumanekas, Christos; Li, Ying; Liu, Wing Kam; Kröger, Martin; Schieber, Jay D.

2014-01-01

We present a method to map the full equilibrium distribution of the primitive-path (PP) length, obtained from multi-chain simulations of polymer melts, onto a single-chain mean-field ‘target’ model. Most previous works used the Doi-Edwards tube model as a target. However, the average number of monomers per PP segment, obtained from multi-chain PP networks, has consistently shown a discrepancy of a factor of two with respect to tube-model estimates. Part of the problem is that the tube model neglects fluctuations in the lengths of PP segments, the number of entanglements per chain and the distribution of monomers among PP segments, while all these fluctuations are observed in multi-chain simulations. Here we use a recently proposed slip-link model, which includes fluctuations in all these variables as well as in the spatial positions of the entanglements. This turns out to be essential to obtain qualitative and quantitative agreement with the equilibrium PP-length distribution obtained from multi-chain simulations. By fitting this distribution, we are able to determine two of the three parameters of the model, which govern its equilibrium properties. This mapping is executed for four different linear polymers and for different molecular weights. The two parameters are found to depend on chemistry, but not on molecular weight. The model predicts a constant plateau modulus minus a correction inversely proportional to molecular weight. The value for well-entangled chains, with the parameters determined ab initio, lies in the range of experimental data for the materials investigated.

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.

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

Biological and surface-active properties of double-chain cationic amino acid-based surfactants.

PubMed

Greber, Katarzyna E; Dawgul, Małgorzata; Kamysz, Wojciech; Sawicki, Wiesław; Łukasiak, Jerzy

2014-08-01

Cationic amino acid-based surfactants were synthesized via solid phase peptide synthesis and terminal acylation of their α and ε positions with saturated fatty acids. Five new lipopeptides, N-α-acyl-N-ε-acyl lysine analogues, were obtained. Minimum inhibitory concentration and minimum bactericidal (fungicidal) concentration were determined on reference strains of bacteria and fungi to evaluate the antimicrobial activity of the lipopeptides. Toxicity to eukaryotic cells was examined via determination of the haemolytic activities. The surface-active properties of these compounds were evaluated by measuring the surface tension and formation of micelles as a function of concentration in aqueous solution. The cationic surfactants demonstrated diverse antibacterial activities dependent on the length of the fatty acid chain. Gram-negative bacteria and fungi showed a higher resistance than Gram-positive bacterial strains. It was found that the haemolytic activities were also chain length-dependent values. The surface-active properties showed a linear correlation between the alkyl chain length and the critical micelle concentration.

Insulin fibrillation and protein design: topological resistance of single-chain analogs to thermal degradation with application to a pump reservoir.

PubMed

Phillips, Nelson B; Whittaker, Jonathan; Ismail-Beigi, Faramarz; Weiss, Michael A

2012-03-01

Insulin is susceptible to thermal fibrillation, a misfolding process that leads to nonnative cross-β assembly analogous to pathological amyloid deposition. Pharmaceutical formulations are ordinarily protected from such degradation by sequestration of the susceptible monomer within native protein assemblies. With respect to the safety and efficacy of insulin pumps, however, this strategy imposes an intrinsic trade-off between pharmacokinetic goals (rapid absorption and clearance) and the requisite physical properties of a formulation (prolonged shelf life and stability within the reservoir). Available rapid-acting formulations are suboptimal in both respects; susceptibility to fibrillation is exacerbated even as absorption is delayed relative to the ideal specifications of a closed-loop system. To circumvent this molecular trade-off, we exploited structural models of insulin fibrils and amyloidogenic intermediates to define an alternative protective mechanism. Single-chain insulin (SCI) analogs were shown to be refractory to thermal fibrillation with maintenance of biological activity for more than 3 months under conditions that promote the rapid fibrillation and inactivation of insulin. The essential idea exploits an intrinsic incompatibility between SCI topology and the geometry of cross-β assembly. A peptide tether was thus interposed between the A- and B-chains whose length was (a) sufficiently long to provide the "play" needed for induced fit of the hormone on receptor binding and yet (b) sufficiently short to impose a topological barrier to fibrillation. Our findings suggest that ultrastable monomeric SCI analogs may be formulated without protective self-assembly and so permit simultaneous optimization of pharmacokinetics and reservoir life. © 2012 Diabetes Technology Society.

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.

Determination of oligomeric chain length distributions at surfaces using ToF-SIMS: segregation effects and polymer properties

NASA Astrophysics Data System (ADS)

Gardella, Joseph A.; Mahoney, Christine M.

2004-06-01

While many XPS and SIMS studies of polymers have detected and quantified segregation of low surface energy blocks or components in copolymers and polymer blends [D. Briggs, in: D.R. Clarke, S. Suresh, I.M. Ward (Eds.), Surface Analysis of Polymers by XPS and Static SIMS, Cambridge University Press, Cambridge, 1998 (Chapter 5).], this paper reports ToF-SIMS studies of direct measurement of the segment length distribution at the surface of siloxane copolymers. These data allow insight into the segregation of particular portions of the oligomeric distribution; specifically, in this study, longer PDMS oligomers segregated at the expense of shorter PDMS chains. We have reported XPS analysis of competitive segregation effects for short PDMS chains [Macromolecules 35 (13) (2002) 5256]. In this study, a series of poly(ureaurethane)-poly(dimethylsiloxane) (PUU-PDMS) copolymers have been synthesized containing varying ratios of G-3 and G-9 (G- X describes the average segment length of the PDMS added), while maintaining a constant overall siloxane weight percentage (10, 30, and 60%). These copolymers were utilized as model systems to study the preferential segregation of certain siloxane segment lengths to the surface over others. ToF-SIMS analysis of PUU-PDMS copolymers has yielded high-mass range copolymer fragmentation patterns containing intact PDMS segments. For the first time, this information is utilized to determine PDMS segment length distributions at the copolymer surface as compared to the bulk. The results show that longer siloxane segment lengths are preferentially segregating to the surface over shorter chain lengths. These results also show the importance of ToF-SIMS and mass spectrometry in the development of new materials containing low molecular weight amino-propyl-terminated siloxanes.

Supramolecular liquid crystalline π-conjugates: the role of aromatic π-stacking and van der Waals forces on the molecular self-assembly of oligophenylenevinylenes.

PubMed

Goel, Mahima; Jayakannan, M

2010-10-07

Here, we report a unique design strategy to trace the role of aromatic π-stacking and van der Waals interactions on the molecular self-organization of π-conjugated building blocks in a single system. A new series of bulky oligophenylenevinylenes (OPVs) bearing a tricyclodecanemethylene (TCD) unit in the aromatic π-core with flexible long methylene chains (n = 0-12 and 16) in the longitudinal position were designed and synthesized. The OPVs were found to be liquid crystalline, and their enthalpies of phase transitions (also entropies) showed odd-even oscillation with respect to the number of carbon atoms in alkyl chains. OPVs with an even number of methylene units in the side chains showed higher enthalpies with respect to their highly packed solid structures compared to odd-numbered ones. Polarized light microscopic analysis confirmed the formation of cholesteric liquid crystalline (LC) phases of fan shaped textures with focal conics in OPVs with 5 ≤ n ≤ 9. OPVs with longer alkyl chains (OPV-10 to OPV-12) produced a birefringence pattern consisting of dark and bright ring-banded suprastructures. The melting temperature followed a sigmoidal trend, indicating the transformation of molecular self-organization in OPVs from solid to ring-banded suprastructures via cholesteric LC intermediates. At longer alkyl chain lengths, the van der Waals interactions among the alkyl chains became predominant and translated the mesogenic effect across the lamellae; as a consequence, the lamellae underwent twisted self-organization along the radial growth direction of the spherulites to produce bright and dark bands. Scanning electron microscope (SEM) analysis of cholesteric LC and ring-banded textures strongly supported the existence of twisted lamellae in the OPVs with ring-banded textures. Variable temperature X-ray diffraction analysis confirmed the reversibility of the molecular self-organization in the solid state and also showed the existence of the higher ordered lamellar structure in ring-banded OPVs. Photophysical characterizations such as excitation, emission, and time resolved fluorescence decay measurements were employed to trace molecular self-organization in their liquid crystalline phases. The emission spectra of the OPV samples showed odd-even oscillation in their emission wavelengths with respect to the length of alkyl chains. Highly packed even-OPVs showed more blue shift compared to that of less crystalline odd-OPVs. Time dependent fluorescence decay of OPVs followed a biexponential fit, and their lifetimes (τ(1) and τ(2) values) revealed that the decay is faster for odd-OPVs compared to even-OPVs. Among all the OPVs, the τ(2) values for OPV-8 and OPV-12 were found to be much higher, indicating their high luminescent characteristics. In a nut shell, bulky liquid crystalline OPV chromophores were cleverly utilized, for the first time, to probe the aromatic π-stacking versus van der Waals interactions on the molecular self-organization of π-conjugated system.

Intermediate scattering function of an anisotropic active Brownian particle

PubMed Central

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-01-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations. PMID:27830719

Intermediate scattering function of an anisotropic active Brownian particle.

PubMed

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-10

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

Intermediate scattering function of an anisotropic active Brownian particle

NASA Astrophysics Data System (ADS)

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

Supramolecular Packing Controls H 2 Photocatalysis in Chromophore Amphiphile Hydrogels

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

Weingarten, Adam S.; Kazantsev, Roman V.; Palmer, Liam C.

2015-11-21

Light harvesting supramolecular assemblies are potentially useful structures as components of solar-to-fuel conversion materials. The development of these functional constructs requires an understanding of optimal packing modes for chromophores. We investigated here assembly in water and the photocatalytic function of perylene monoimide chromophore amphiphiles with different alkyl linker lengths separating their hydrophobic core and the hydrophilic carboxylate headgroup. We found that these chromophore amphiphiles (CAs) self-assemble into charged nanostructures of increasing aspect ratio as the linker length is increased. The addition of salt to screen the charged nanostructures induced the formation of hydrogels and led to internal crystallization within somemore » of the nanostructures. For linker lengths up to seven methylenes, the CAs were found to pack into 2D crystalline unit cells within ribbon-shaped nanostructures, whereas the nine methylene CAs assembled into long nanofibers without crystalline molecular packing. At the same time, the different molecular packing arrangements after charge screening led to different absorbance spectra, despite the identical electronic properties of all PMI amphiphiles. While the crystalline CAs formed electronically coupled H-aggregates, only CAs with intermediate linker lengths showed evidence of high intermolecular orbital overlap. Photocatalytic hydrogen production using a nickel-based catalyst was observed in all hydrogels, with the highest turnovers observed for CA gels having intermediate linker lengths. We conclude that the improved photocatalytic performance of the hydrogels formed by supramolecular assemblies of the intermediate linker CA molecules likely arises from improved exciton splitting efficiencies due to their higher orbital overlap.« less

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

The giant African snail Achatina fulica as natural intermediate host of Angiostrongylus cantonensis in Pernambuco, northeast Brazil.

PubMed

Thiengo, S C; Maldonado, A; Mota, E M; Torres, E J L; Caldeira, R; Carvalho, O S; Oliveira, A P M; Simões, R O; Fernandez, M A; Lanfredi, R M

2010-09-01

The human cases of eosinophilic meningitis recently reported from Brazil have focused the attention of the public health agencies on the role the introduced snail Achatina fulica plays as hosts of the metastrongylid nematodes. Determining the potential of this snail to host and develop infective larval stages of metastrongylids in the wild and identify the species harbored by them is crucial for designing effective control measures. Here we assess if A. fulica may act as intermediate host of A. cantonensis at the peridomiciliary areas of a patient's house from state of Pernambuco (PE), who was diagnosed with eosinophilic meningitis and a history of ingesting raw molluscs. Larvae obtained from naturally infected A. fulica were orally administered to Rattus norvegicus. The worms were collected from the pulmonary artery and brain, and were morphologically characterized and compared to the Japan isolate of A. cantonensis. Adult worms and infective L(3) larvae (PE isolate) recovered from A. fulica specimens were also analyzed by polymerase chain reaction and restriction fragment length polymorphism of ITS2 region from rDNA and compared to A. cantonensis (ES isolate), A. vasorum (MG isolate) and A. costaricensis (RS isolate). The large size of the spicules (greater than those observed in other species of Angiostrongylus) and the pattern of the bursal rays agree with the original species description by Chen (1935). Furthermore, the morphology of the PE isolate was similar to that of Japan isolate. The PCR-RFLP profiles obtained were distinctive among species and no variation in patterns was detected among adult individuals from A. cantonensis isolates from PE and ES. The importance of A. fulica as an intermediate host of eosinophilic menigoencepahlitis in Brazil is emphasized. 2010 Elsevier B.V. All rights reserved.

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.

What Have Metabolomics Approaches Taught Us About Type 2 Diabetes?

PubMed

Gonzalez-Franquesa, Alba; Burkart, Alison M; Isganaitis, Elvira; Patti, Mary-Elizabeth

2016-08-01

Type 2 diabetes (T2D) is increasing worldwide, making identification of biomarkers for detection, staging, and effective prevention strategies an especially critical scientific and medical goal. Fortunately, advances in metabolomics techniques, together with improvements in bioinformatics and mathematical modeling approaches, have provided the scientific community with new tools to describe the T2D metabolome. The metabolomics signatures associated with T2D and obesity include increased levels of lactate, glycolytic intermediates, branched-chain and aromatic amino acids, and long-chain fatty acids. Conversely, tricarboxylic acid cycle intermediates, betaine, and other metabolites decrease. Future studies will be required to fully integrate these and other findings into our understanding of diabetes pathophysiology and to identify biomarkers of disease risk, stage, and responsiveness to specific treatments.

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.

Examination of food chain-derived Listeria monocytogenes strains of different serotypes reveals considerable diversity in inlA genotypes, mutability, and adaptation to cold temperatures.

PubMed

Kovacevic, Jovana; Arguedas-Villa, Carolina; Wozniak, Anna; Tasara, Taurai; Allen, Kevin J

2013-03-01

Listeria monocytogenes strains belonging to serotypes 1/2a and 4b are frequently linked to listeriosis. While inlA mutations leading to premature stop codons (PMSCs) and attenuated virulence are common in 1/2a, they are rare in serotype 4b. We observed PMSCs in 35% of L. monocytogenes isolates (n = 54) recovered from the British Columbia food supply, including serotypes 1/2a (30%), 1/2c (100%), and 3a (100%), and a 3-codon deletion (amino acid positions 738 to 740) seen in 57% of 4b isolates from fish-processing facilities. Caco-2 invasion assays showed that two isolates with the deletion were significantly more invasive than EGD-SmR (P < 0.0001) and were either as (FF19-1) or more (FE13-1) invasive than a clinical control strain (08-5578) (P = 0.006). To examine whether serotype 1/2a was more likely to acquire mutations than other serotypes, strains were plated on agar with rifampin, revealing 4b isolates to be significantly more mutable than 1/2a, 1/2c, and 3a serotypes (P = 0.0002). We also examined the ability of 33 strains to adapt to cold temperature following a downshift from 37°C to 4°C. Overall, three distinct cold-adapting groups (CAG) were observed: 46% were fast (<70 h), 39% were intermediate (70 to 200 h), and 15% were slow (>200 h) adaptors. Intermediate CAG strains (70%) more frequently possessed inlA PMSCs than did fast (20%) and slow (10%) CAGs; in contrast, 87% of fast adaptors lacked inlA PMSCs. In conclusion, we report food chain-derived 1/2a and 4b serotypes with a 3-codon deletion possessing invasive behavior and the novel association of inlA genotypes encoding a full-length InlA with fast cold-adaptation phenotypes.

Engineering Pseudomonas putida KT2440 for Efficient Ethylene Glycol Utilization

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

Beckham, Gregg T; Franden, Mary A; Thelhawadigedara, Lahiru Niroshan Jayakody

Ethylene glycol is used as a raw material in the production of polyethylene terephthalate, in antifreeze, as a gas hydrate inhibitor in pipelines, and for many other industrial applications. It is metabolized by aerobic microbial processes via the highly toxic intermediates glycolaldehyde and glycolate through C2 metabolic pathways. Pseudomonas putida KT2440, which has been engineered for environmental remediation applications given its high toxicity tolerance and broad substrate specificity, is not able to efficiently metabolize ethylene glycol, despite harboring putative genes for this purpose. To further expand the metabolic portfolio of P. putida, we elucidated the metabolic pathway to enable ethylenemore » glycol via systematic overexpression of glyoxylate carboligase (gcl) in combination with other genes. Quantitative reverse transcription polymerase chain reaction demonstrated that all of the four genes in genomic proximity to gcl (hyi, glxR, ttuD, and pykF) are transcribed as an operon. Where the expression of only two genes (gcl and glxR) resulted in growth in ethylene glycol, improved growth and ethylene glycol utilization were observed when the entire gcl operon was expressed. Both glycolaldehyde and glyoxal inhibit growth in concentrations of ethylene glycol above 50 mM. To overcome this bottleneck, the additional overexpression of the glycolate oxidase (glcDEF) operon removes the glycolate bottleneck and minimizes the production of these toxic intermediates, permitting growth in up to 2 M (~124 g/L) and complete consumption of 0.5 M (31 g/L) ethylene glycol in shake flask experiments. In addition, the engineered strain enables conversion of ethylene glycol to medium-chain-length polyhydroxyalkanoates (mcl-PHAs). Overall, this study provides a robust P. putida KT2440 strain for ethylene glycol consumption, which will serve as a foundational strain for further biocatalyst development for applications in the remediation of waste polyester plastics and biomass-derived wastewater streams.« less

Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization.

PubMed

Franden, Mary Ann; Jayakody, Lahiru N; Li, Wing-Jin; Wagner, Neil J; Cleveland, Nicholas S; Michener, William E; Hauer, Bernhard; Blank, Lars M; Wierckx, Nick; Klebensberger, Janosch; Beckham, Gregg T

2018-06-07

Ethylene glycol is used as a raw material in the production of polyethylene terephthalate, in antifreeze, as a gas hydrate inhibitor in pipelines, and for many other industrial applications. It is metabolized by aerobic microbial processes via the highly toxic intermediates glycolaldehyde and glycolate through C2 metabolic pathways. Pseudomonas putida KT2440, which has been engineered for environmental remediation applications given its high toxicity tolerance and broad substrate specificity, is not able to efficiently metabolize ethylene glycol, despite harboring putative genes for this purpose. To further expand the metabolic portfolio of P. putida, we elucidated the metabolic pathway to enable ethylene glycol via systematic overexpression of glyoxylate carboligase (gcl) in combination with other genes. Quantitative reverse transcription polymerase chain reaction demonstrated that all of the four genes in genomic proximity to gcl (hyi, glxR, ttuD, and pykF) are transcribed as an operon. Where the expression of only two genes (gcl and glxR) resulted in growth in ethylene glycol, improved growth and ethylene glycol utilization were observed when the entire gcl operon was expressed. Both glycolaldehyde and glyoxal inhibit growth in concentrations of ethylene glycol above 50 mM. To overcome this bottleneck, the additional overexpression of the glycolate oxidase (glcDEF) operon removes the glycolate bottleneck and minimizes the production of these toxic intermediates, permitting growth in up to 2 M (~124 g/L) and complete consumption of 0.5 M (31 g/L) ethylene glycol in shake flask experiments. In addition, the engineered strain enables conversion of ethylene glycol to medium-chain-length polyhydroxyalkanoates (mcl-PHAs). Overall, this study provides a robust P. putida KT2440 strain for ethylene glycol consumption, which will serve as a foundational strain for further biocatalyst development for applications in the remediation of waste polyester plastics and biomass-derived wastewater streams. Copyright © 2018. Published by Elsevier Inc.

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

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.

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.

Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres

PubMed Central

Gronau, Greta; Jacobsen, Matthew M.; Huang, Wenwen; Rizzo, Daniel J.; Li, David; Staii, Cristian; Pugno, Nicola M.; Wong, Joyce Y.; Kaplan, David L.; Buehler, Markus J.

2016-01-01

Scalable computational modelling tools are required to guide the rational design of complex hierarchical materials with predictable functions. Here, we utilize mesoscopic modelling, integrated with genetic block copolymer synthesis and bioinspired spinning process, to demonstrate de novo materials design that incorporates chemistry, processing and material characterization. We find that intermediate hydrophobic/hydrophilic block ratios observed in natural spider silks and longer chain lengths lead to outstanding silk fibre formation. This design by nature is based on the optimal combination of protein solubility, self-assembled aggregate size and polymer network topology. The original homogeneous network structure becomes heterogeneous after spinning, enhancing the anisotropic network connectivity along the shear flow direction. Extending beyond the classical polymer theory, with insights from the percolation network model, we illustrate the direct proportionality between network conductance and fibre Young's modulus. This integrated approach provides a general path towards de novo functional network materials with enhanced mechanical properties and beyond (optical, electrical or thermal) as we have experimentally verified. PMID:26017575

Predictive modelling-based design and experiments for synthesis and spinning of bioinspired silk fibres.

PubMed

Lin, Shangchao; Ryu, Seunghwa; Tokareva, Olena; Gronau, Greta; Jacobsen, Matthew M; Huang, Wenwen; Rizzo, Daniel J; Li, David; Staii, Cristian; Pugno, Nicola M; Wong, Joyce Y; Kaplan, David L; Buehler, Markus J

2015-05-28

Scalable computational modelling tools are required to guide the rational design of complex hierarchical materials with predictable functions. Here, we utilize mesoscopic modelling, integrated with genetic block copolymer synthesis and bioinspired spinning process, to demonstrate de novo materials design that incorporates chemistry, processing and material characterization. We find that intermediate hydrophobic/hydrophilic block ratios observed in natural spider silks and longer chain lengths lead to outstanding silk fibre formation. This design by nature is based on the optimal combination of protein solubility, self-assembled aggregate size and polymer network topology. The original homogeneous network structure becomes heterogeneous after spinning, enhancing the anisotropic network connectivity along the shear flow direction. Extending beyond the classical polymer theory, with insights from the percolation network model, we illustrate the direct proportionality between network conductance and fibre Young's modulus. This integrated approach provides a general path towards de novo functional network materials with enhanced mechanical properties and beyond (optical, electrical or thermal) as we have experimentally verified.

Floating phase in the one-dimensional transverse axial next-nearest-neighbor Ising model.

PubMed

Chandra, Anjan Kumar; Dasgupta, Subinay

2007-02-01

To study the ground state of an axial next-nearest-neighbor Ising chain under transverse field as a function of frustration parameter kappa and field strength Gamma, we present here two different perturbative analyses. In one, we consider the (known) ground state at kappa=0.5 and Gamma=0 as the unperturbed state and treat an increase of the field from 0 to Gamma coupled with an increase of kappa from 0.5 to 0.5+rGamma/J as perturbation. The first-order perturbation correction to eigenvalue can be calculated exactly and we could conclude that there are only two phase-transition lines emanating from the point kappa=0.5, Gamma=0. In the second perturbation scheme, we consider the number of domains of length 1 as the perturbation and obtain the zeroth-order eigenfunction for the perturbed ground state. From the longitudinal spin-spin correlation, we conclude that floating phase exists for small values of transverse field over the entire region intermediate between the ferromagnetic phase and antiphase.

Structure and properties of starches from Arracacha (Arracacia xanthorrhiza) roots.

PubMed

Castanha, Nanci; Villar, James; Matta Junior, Manoel Divino da; Anjos, Carlota Boralli Prudente Dos; Augusto, Pedro Esteves Duarte

2018-06-05

Arracacha (Arracacia xanthorrhiza Bancroft) is an underexplored Andean root with a high starch content. In this work, starches from two different varieties of Peruvian arracacha were evaluated and characterized in relation to their granule morphology, molecular structure and properties. The starches presented round or polygonal shapes, with a mean diameter of ~20 μm and B-type granules. They were rich in amylopectin molecules with long chain lengths (with the ability to complex iodine) and some with intermediate sizes (indicating a defective crystalline structure). The starches presented low gelatinization temperature, enthalpy of gelatinization and tendency to retrogradation and high peak apparent viscosity and swelling capacity, even at moderate temperatures (60 °C), characteristics of high interest for industrial purposes. Besides, the starches presented a smooth and elastic gel and a high paste clarity. Overall, the arracacha roots presented attractive properties and can be used as an alternative botanical source for starch extraction. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis of opioidmimetics, 3-[H-Dmt-NH(CH(2))(m)]-6-[H-Dmt-NH(CH(2))(n)]-2(1H)-pyrazinones, and studies on structure-activity relationships.

PubMed

Shiotani, Kimitaka; Miyazaki, Anna; Li, Tingyou; Tsuda, Yuko; Yokoi, Toshio; Ambo, Akihiro; Sasaki, Yusuke; Bryant, Sharon D; Jinsmaa, Yunden; Lazarus, Lawrence H; Okada, Yoshio

2007-11-01

Opioidmimetics containing 3-[H-Dmt-NH-(CH(2))(m)]-6-[H-Dmt-NH-(CH(2))(n)]-2(1H)-pyrazinone symmetric (m = n, 1-4) (1 - 4) and asymmetric (m, n = 1 - 4) aliphatic chains (5 - 16) were synthesized using dipeptidyl chloromethylketone intermediates. They had high mu-affinity (K(i)mu = 0.021 - 2.94 nM), delta-affinity (K(i)delta = 1.06 - 152.6 nM), and mu selectivity (K(i)delta/K(i)mu = 14 - 3,126). The opioidmimetics (1 - 16) exhibited mu agonism in proportion to their mu-receptor affinity. delta-Agonism was essentially lacking in the compounds except (4) and (16), and (1) and (2) indicated weak delta antagonism (pA(2) = 6.47 and 6.56, respectively). The data verify that a specific length of aliphatic linker is required between the Dmt pharmacophore and the pyrazinone ring to produce unique mu-opioid receptor ligands.

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.

[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

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

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.

Pentadecanoic and Heptadecanoic Acids: Multifaceted Odd-Chain Fatty Acids12

PubMed Central

Pfeuffer, Maria; Jaudszus, Anke

2016-01-01

The odd-chain fatty acids (OCFAs) pentadecanoic acid (15:0) and heptadecanoic acid (17:0), which account for only a small proportion of total saturated fatty acids in milk fat and ruminant meat, are accepted biomarkers of dairy fat intake. However, they can also be synthesized endogenously, for example, from gut-derived propionic acid (3:0). A number of studies have shown an inverse association between OCFA concentrations in human plasma phospholipids or RBCs and risk of type 2 diabetes and cardiovascular disease. We propose a possible involvement in metabolic regulation from the assumption that there is a link between 15:0 and 17:0 and the metabolism of other short-chain, medium-chain, and longer-chain OCFAs. The OCFAs 15:0 and 17:0 can be elongated to very-long-chain FAs (VLCFAs) such as tricosanoic acid (23:0) and pentacosanoic acid (25:0) in glycosphingolipids, particularly found in brain tissue, or can be derived from these VLCFAs. Their chains can be shortened, yielding propionyl-coenzyme A (CoA). Propionyl-CoA, by succinyl-CoA, can replenish the citric acid cycle (CAC) with anaplerotic intermediates and, thus, improve mitochondrial energy metabolism. Mitochondrial function is compromised in a number of disorders and may be impaired with increasing age. Optimizing anaplerotic intermediate availability for the CAC may help to cope with demands in times of increased metabolic stress and with aging. OCFAs may serve as substrates for synthesis of both odd-numbered VLCFAs and propionyl-CoA or store away excess propionic acid. PMID:27422507

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

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.

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.

Improving Orientation Outcomes: Implementation of Phased Orientation Process in an Intermediate Special Care Nursery.

PubMed

Rivera, Emily K; Shedenhelm, Heidi J; Gibbs, Ardyce L

2015-01-01

In response to changing needs of registered nurse orientees, the staff education committee in the Intermediate Special Care Nursery has implemented a phased orientation process. This phased process includes a mentoring experience postorientation to support a new nurse through the first year of employment. Since implementing the phased orientation process in the Intermediate Special Care Nursery, orientee satisfaction and preparation to practice have increased, and length of orientation has decreased.

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.

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.

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.

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.

PubMed

Zhang, Hua; Zhang, Tuo; Gao, Jianzhao; Ruan, Jishou; Shen, Shiyi; Kurgan, Lukasz

2012-01-01

Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.

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.

Relationship between vegetation coverage and abundance, size, and diet of juvenile largemouth bass during winter

USGS Publications Warehouse

Miranda, L.E.; Pugh, L.L.

1997-01-01

Juvenile largemouth bass Micropterus salmoides were collected by electrofishing during October through March 1992-1994 from coves (???25 ha) covered with aquatic macrophytes over 1-65% of their area. Mean total length of juvenile largemouth bass was highest in coves with the least vegetated cover, but increase in mean length between October and March was highest in coves having near 20% vegetation coverage. Catch per unit effort decreased between October and March; decreases were least at vegetation coverages near 10-20%, highest at coverages of 5% or less, and intermediate at coverages of 30-65%. By March, these disparate decreases contributed to the formation of a dome-like relationship between vegetation coverage and catch per unit effort. Consumption of fish foods was highest when vegetation coverage was low, but decreased asymptotically as coverage increased; consumption of invertebrate foods increased at low coverage, peaked near 20-30% coverage, and decreased at higher coverage. We suggest that greater length increases and greater abundance at 10-25% vegetation coverage were stimulated by a favorable blend of food availability and cover. Our results support reports that maximum recruitment of largemouth bass occurs at intermediate levels of vegetation coverage, and we further suggests that such increased production is reinforced during winter, when survival, invertebrate consumption, and length increases are highest at intermediate levels of vegetation coverage.

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

Pathways and intermediates in forced unfolding of spectrin repeats.

PubMed

Altmann, Stephan M; Grünberg, Raik G; Lenne, Pierre-François; Ylänne, Jari; Raae, Arnt; Herbert, Kristina; Saraste, Matti; Nilges, Michael; Hörber, J K Heinrich

2002-08-01

Spectrin repeats are triple-helical coiled-coil domains found in many proteins that are regularly subjected to mechanical stress. We used atomic force microscopy technique and steered molecular dynamics simulations to study the behavior of a wild-type spectrin repeat and two mutants. The experiments indicate that spectrin repeats can form stable unfolding intermediates when subjected to external forces. In the simulations the unfolding proceeded via a variety of pathways. Stable intermediates were associated to kinking of the central helix close to a proline residue. A mutant stabilizing the central helix showed no intermediates in experiments, in agreement with simulation. Spectrin repeats may thus function as elastic elements, extendable to intermediate states at various lengths.

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.

Dynamic cross-correlations between entangled biofilaments as they diffuse

PubMed Central

Tsang, Boyce; Dell, Zachary E.; Jiang, Lingxiang; Schweizer, Kenneth S.; Granick, Steve

2017-01-01

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 104 times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales. PMID:28283664

Magnetization curves of di-, tri- and tetramerized mixed spin-1 and spin-2 Heisenberg chains

NASA Astrophysics Data System (ADS)

Karľová, Katarína; Strečka, Jozef

2018-05-01

Magnetization curves of ferrimagnetic mixed spin-1 and spin-2 Heisenberg chains are calculated with the help of density-matrix renormalization group method and quantum Monte Carlo simulations by considering a spin dimerization (1,2), trimerization (1,1,2) and tetramerization (1,1,1,2). The investigated mixed-spin Heisenberg chains can be alternatively viewed as a pure spin-1 Heisenberg chain, which contains at a regular lattice positions spin-2 particles. Unlike the antiferromagnetic spin-1 Heisenberg chain solely displaying a zero magnetization plateau due to the Haldane phase, the ferrimagnetic mixed spin-(1,2), spin-(1,1,2) and spin-(1,1,1,2) Heisenberg chains exhibit more striking magnetization curves involving at least two intermediate magnetization plateaux and quantum spin-liquid states.

Paramagnetic colloids: Chaotic routes to clusters and molecules

NASA Astrophysics Data System (ADS)

Abdi, Hamed; Soheilian, Rasam; Erb, Randall M.; Maloney, Craig E.

2018-03-01

We present computer simulations and experiments on dilute suspensions of superparamagnetic particles subject to rotating magnetic fields. We focus on chains of four particles and their decay routes to stable structures. At low rates, the chains track the external field. At intermediate rates, the chains break up but perform a periodic (albeit complex) motion. At sufficiently high rates, the chains generally undergo chaotic motion at short times and decay to either closely packed clusters or more dispersed, colloidal molecules at long times. We show that the transition out of the chaotic states can be described as a Poisson process in both simulation and experiment.

Supramolecular Packing Controls H 2 Photocatalysis in Chromophore Amphiphile Hydrogels

DOE PAGES

Weingarten, Adam S.; Kazantsev, Roman V.; Palmer, Liam C.; ...

2015-11-21

Light harvesting supramolecular assemblies are potentially useful structures as components of solar-to-fuel conversion materials. The development of these functional constructs requires an understanding of optimal packing modes for chromophores. Here, we investigated assembly in water and the photocatalytic function of perylene monoimide chromophore amphiphiles with different alkyl linker lengths separating their hydrophobic core and the hydrophilic carboxylate headgroup. We found that these chromophore amphiphiles (CAs) self-assemble into charged nanostructures of increasing aspect ratio as the linker length is increased. The addition of salt to screen the charged nanostructures induced the formation of hydrogels and led to internal crystallization within somemore » of the nanostructures. For linker lengths up to seven methylenes, the CAs were found to pack into 2D crystalline unit cells within ribbon-shaped nanostructures, whereas the nine methylene CAs assembled into long nanofibers without crystalline molecular packing. At the same time, the different molecular packing arrangements after charge screening led to different absorbance spectra, despite the identical electronic properties of all PMI amphiphiles. While the crystalline CAs formed electronically coupled H-aggregates, only CAs with intermediate linker lengths showed evidence of high intermolecular orbital overlap. Photocatalytic hydrogen production using a nickel-based catalyst was observed in all hydrogels, with the highest turnovers observed for CA gels having intermediate linker lengths. Lastly, we conclude that the improved photocatalytic performance of the hydrogels formed by supramolecular assemblies of the intermediate linker CA molecules likely arises from improved exciton splitting efficiencies due to their higher orbital overlap.« less

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.

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.

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.

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

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.

Global stocks of selected mineral-based commodities

USGS Publications Warehouse

Wilburn, David R.; Bleiwas, Donald I.; Karl, Nick A.

2016-12-05

IntroductionThe U.S. Geological Survey, National Minerals Information Center, analyzes mineral and metal supply chains by identifying and describing major components of mineral and material flows from ore extraction, through intermediate forms, to a final product. This report focuses on an important component of the world’s supply chain: the amounts and global distribution of major consumer, producer, and exchange stocks of selected mineral commodities. In this report, the term “stock” is used instead of “inventory” and refers to accumulations of mined ore, intermediate products, and refined mineral-based commodities that are in a form that meets the agreed-upon specifications of a buyer or processor of intermediate products. These may include certain ores such as bauxite, concentrates, smelter products, and refined metals. Materials sometimes referred to as inventory for accounting purposes, such as ore contained in a deposit or in a leach pile, or materials that need to be further processed before they can be shipped to a consumer, are not considered. Stocks may be held (owned) by consumers, governments, investors, producers, and traders. They may serve as (1) a means to achieve economic, social, and strategic goals through government policies; (2) a secure source of supply to meet demand and to mitigate potential shortages in the supply chain; (3) a hedge to mitigate price volatility; and (4) vehicles for speculative investment.The paucity and uneven reliability of data for stocks of ores and concentrates and for material held by producers, consumers, and merchants hinder the accurate estimating of the size and distribution of this portion of the supply chain for certain commodities. This paper reviews the more visible stocks held in commodity exchange warehouses distributed throughout the world.

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

Electronic band gaps of confined linear carbon chains ranging from polyyne to carbyne

NASA Astrophysics Data System (ADS)

Shi, Lei; Rohringer, Philip; Wanko, Marius; Rubio, Angel; Waßerroth, Sören; Reich, Stephanie; Cambré, Sofie; Wenseleers, Wim; Ayala, Paola; Pichler, Thomas

2017-12-01

Ultralong linear carbon chains of more than 6000 carbon atoms have recently been synthesized within double-walled carbon nanotubes (DWCNTs), and they show a promising route to one-atom-wide semiconductors with a direct band gap. Theoretical studies predicted that this band gap can be tuned by the length of the chains, the end groups, and their interactions with the environment. However, different density functionals lead to very different values of the band gap of infinitely long carbyne. In this work, we applied resonant Raman excitation spectroscopy with more than 50 laser wavelengths to determine the band gap of long carbon chains encapsulated inside DWCNTs. The experimentally determined band gaps ranging from 2.253 to 1.848 eV follow a linear relation with Raman frequency. This lower bound is the smallest band gap of linear carbon chains observed so far. The comparison with experimental data obtained for short chains in gas phase or in solution demonstrates the effect of the DWCNT encapsulation, leading to an essential downshift of the band gap. This is explained by the interaction between the carbon chain and the host tube, which greatly modifies the chain's bond-length alternation.

The Impact of Patient Profiles and Procedures on Hospitalization Costs through Length of Stay in Community-Acquired Pneumonia Patients Based on a Japanese Administrative Database

PubMed Central

Uematsu, Hironori; Kunisawa, Susumu; Yamashita, Kazuto; Imanaka, Yuichi

2015-01-01

Background Community-acquired pneumonia is a common cause of patient hospitalization, and its burden on health care systems is increasing in aging societies. In this study, we aimed to investigate the factors that affect hospitalization costs in community-acquired pneumonia patients while considering the intermediate influence of patient length of stay. Methods Using a multi-institutional administrative claims database, we analyzed 30,041 patients hospitalized for community-acquired pneumonia who had been discharged between April 1, 2012 and September 30, 2013 from 289 acute care hospitals in Japan. Possible factors associated with hospitalization costs were investigated using structural equation modeling with length of stay as an intermediate variable. We calculated the direct, indirect (through length of stay), and total effects of the candidate factors on hospitalization costs in the model. Lastly, we calculated the ratio of indirect effects to direct effects for each factor. Results The structural equation model showed that higher disease severities (using A-DROP, Barthel Index, and Charlson Comorbidity Index scores), use of mechanical ventilation, and tube feeding were associated with higher hospitalization costs, regardless of the intermediate influence of length of stay. The severity factors were also associated with longer length of stay durations. The ratio of indirect effects to direct effects on total hospitalization costs showed that the former was greater than the latter in the factors, except in the use of mechanical ventilation. Conclusions Our structural equation modeling analysis indicated that patient profiles and procedures impacted on hospitalization costs both directly and indirectly. Furthermore, the profiles were generally shown to have greater indirect effects (through length of stay) on hospitalization costs than direct effects. These findings may be useful in supporting the more appropriate distribution of health care resources. PMID:25923785

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.

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.

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.

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

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…

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.

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.

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.

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.

Bacterial Polysaccharide Co-Polymerases Share a Common Framework for Control of Polymer Length

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

Tocilj,A.; Munger, C.; Proteau, A.

2008-01-01

The chain length distribution of complex polysaccharides present on the bacterial surface is determined by polysaccharide co-polymerases (PCPs) anchored in the inner membrane. We report crystal structures of the periplasmic domains of three PCPs that impart substantially different chain length distributions to surface polysaccharides. Despite very low sequence similarities, they have a common protomer structure with a long central alpha-helix extending 100 Angstroms into the periplasm. The protomers self-assemble into bell-shaped oligomers of variable sizes, with a large internal cavity. Electron microscopy shows that one of the full-length PCPs has a similar organization as that observed in the crystal formore » its periplasmic domain alone. Functional studies suggest that the top of the PCP oligomers is an important region for determining polysaccharide modal length. These structures provide a detailed view of components of the bacterial polysaccharide assembly machinery.« less

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.

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.

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.

A Finite Length Cylinder Model for Mixed Oxide-Ion and Electron Conducting Cathodes Suited for Intermediate-Temperature Solid Oxide Fuel Cells

DOE PAGES

Jin, Xinfang; Wang, Jie; Jiang, Long; ...

2016-03-25

A physics-based model is presented to simulate the electrochemical behavior of mixed ion and electron conducting (MIEC) cathodes for intermediate-temperature solid oxide fuel cells. Analytic solutions for both transient and impedance models based on a finite length cylinder are derived. These solutions are compared to their infinite length counterparts. The impedance solution is also compared to experimental electrochemical impedance spectroscopy data obtained from both a traditional well-established La 0.6Sr 0.4Co 0.2Fe 0.8O 3-δ (LSCF) cathode and a new SrCo 0.9Nb 0.1O 3-δ (SCN) porous cathode. Lastly, the impedance simulations agree well with the experimental values, demonstrating that the new modelsmore » can be used to extract electro-kinetic parameters of MIEC SOFC cathodes.« less

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

PubMed Central

Kannan, Srinivasaraghavan; Zacharias, Martin

2014-01-01

The 20 residue Trp-cage mini-protein is one of smallest proteins that adopt a stable folded structure containing also well-defined secondary structure elements. The hydrophobic core is arranged around a single central Trp residue. Despite several experimental and simulation studies the detailed folding mechanism of the Trp-cage protein is still not completely understood. Starting from fully extended as well as from partially folded Trp-cage structures a series of molecular dynamics simulations in explicit solvent and using four different force fields was performed. All simulations resulted in rapid collapse of the protein to on average relatively compact states. The simulations indicate a significant dependence of the speed of folding to near-native states on the side chain rotamer state of the central Trp residue. Whereas the majority of intermediate start structures with the central Trp side chain in a near-native rotameric state folded successfully within less than 100 ns only a fraction of start structures reached near-native folded states with an initially non-native Trp side chain rotamer state. Weak restraining of the Trp side chain dihedral angles to the state in the folded protein resulted in significant acceleration of the folding both starting from fully extended or intermediate conformations. The results indicate that the side chain conformation of the central Trp residue can create a significant barrier for controlling transitions to a near native folded structure. Similar mechanisms might be of importance for the folding of other protein structures. PMID:24563686

Spot-shadowing optimization to mitigate damage growth in a high-energy-laser amplifier chain.

PubMed

Bahk, Seung-Whan; Zuegel, Jonathan D; Fienup, James R; Widmayer, C Clay; Heebner, John

2008-12-10

A spot-shadowing technique to mitigate damage growth in a high-energy laser is studied. Its goal is to minimize the energy loss and undesirable hot spots in intermediate planes of the laser. A nonlinear optimization algorithm solves for the complex fields required to mitigate damage growth in the National Ignition Facility amplifier chain. The method is generally applicable to any large fusion laser.

Molecular dynamics study of intermediate phase of long chain alkyl sulfonate/water systems.

PubMed

Poghosyan, Armen H; Arsenyan, Levon H; Shahinyan, Aram A

2013-01-08

Using atomic level simulation we aimed to investigate various intermediate phases of the long chain alkyl sulfonate/water system. Overall, about 800 ns parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 128 sodium pentadecyl sulfonate and 2251 water molecules. The GROMACS software code with united atom force field was applied. Despite some differences, the analysis of main structural parameters is in agreement with X-ray experimental findings. The mechanism of self-assembly of SPDS molecules was also examined. At T = 323 K we obtained both tilted fully interdigitated and liquid crystalline-like disordered hydrocarbon chains; hence, the presence of either gel phase that coexists with a lamellar phase or metastable gel phase with fraction of gauche configuration can be assumed. Further increase of temperature revealed that the system underwent a transition to a lamellar phase, which was clearly identified by the presence of fully disordered hydrocarbon chains. The transition from gel-to-fluid phase was implemented by simulated annealing treatment, and the phase transition point at T = 335 K was identified. The surfactant force field in its presented set is surely enabled to fully demonstrate the mechanism of self-assembly and the behavior of phase transition making it possible to get important information around the phase transition point.

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.

Thermodynamic and kinetic control of charged, amphiphilic triblock copolymer assembly via interaction with organic counterions in solvent mixtures

NASA Astrophysics Data System (ADS)

Cui, Honggang

2007-12-01

Amphiphilic block copolymers, consisting of at least two types of monomers with different affinity to the dissolving solvent(s), have been recognized as a molecular building unit for their chemical tunability and design flexibility. Amphiphilic block copolymers with a chargeable block have structural features of polyelectrolytes, block copolymers and surfactants. The combination of these different features offers great flexibility for developing novel assembled morphologies at the nanoscale and outstanding ability to control and manipulate those morphologies. The nanostructures, formed from the spontaneous association of amphiphilic block copolymer in selective solvents, show promise for applications in nanotechnology and pharmaceuticals, including drug delivery, tissue engineering and bio-imaging. A basic knowledge of their modes of self-assembly and their correspondence to application-related properties is just now being developed and poses a considerable scientific challenge. The goal of this dissertation is to investigate the associative behavior of charged, amphiphilic block copolymers in solvent mixtures while in the presence of organic counterions. Self-assembly of poly (acrylic acid)- block-poly (methyl acrylate)-block-polystyrene (PAA- b-PMA-b-PS) triblock copolymers produces nanodomains in THF/water solution specifically through the interaction with organic counterions (polyamines). These assembled structures can include classic micelles (spheres, cylinders and vesicles), but, more importantly, include non-classic micelles (disks, toroids, branched micelles and segmented micelles). Each micelle structure is stable and reproducible at different assembly conditions. The assembled micellar structures depend on not only solution components (thermodynamics) but also mixing procedure and consequent self-assembly pathway (kinetics). The key factors that determine the thermodynamic interactions that partially define the assembled structures and the kinetic assembly process include THF/water ratio, PS block length, the type and amount of organic counterions, and the mixing pathway. Their formation mechanism has been investigated from three aspects: (i) the chain structure of organic counterions, including spacer length, chain hydrophobicity between ionizable groups and the number of ionizable groups (amine group); (ii) molecular structure of the triblock copolymer, including block length of polystyrene and chain architecture; (iii) relative variation of the components, such as different ratios of THF to water and the different ratios of amine groups to acid groups. The first example of a novel micelle formed was the toroidal micelle. The toroidal micelle morphology, which is theoretically predicted but rarely observed, has been produced by the self assembly of PAA99- b-PMA73-b-PS66 in combination with 2,2-(ethylenedioxy)diethylamine (EDDA) and mixed THF/H2O solvent. It was found that toroids can be constructed by two mechanisms: elimination of energetically unfavored cylindrical micelle endcaps or perforation of disk-like micelles. Three-fold junctions were formed as intermediate structures to facilitate toroidal formation from cylindrical micelles. In order to construct toroids from cylindrical micelles, three requirements must be met: lower bending modulus (flexibility of cylinders), selfattraction between cylinders, and extra endcapping energy originating from chain packing frustration. Extremely high energy spheres can also fuse into toroids. Disk-like micelles can transform into a toroidal morphology when cylindrical packing geometry was initiated along the rims of disk-like micelles via solvent mixing that eventually perforated the disk center. The toroidal morphology can be kinetically trapped by either ridding the system of organic solvent or chemically crosslinking the PAA corona with EDDA via addition of 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide methiodide (DPEM). The interaction of positively-charged, multivalent organic amines with the negatively-charged PAA corona plays a decisive role in the formation of these micelles. Inter-chain binding from the interaction of the two amine end groups of diamines with acid groups from different PAA corona blocks governs the final assembled structures. Diamines with hydrophilic spacers induced the formation of micelles with larger interfacial curvature as the spacer length increased. Disk-like micelles, cylindrical micelles or spherical micelles were observed with the gradual increase of hydrophilic spacer length. Diamines with variable hydrophobic spacers showed a similar effect when the spacer length was less than six methylene units. Application of longer hydrophobic diamines had a reverse effect on the interfacial curvature. This effect was attributed to the interaction of hydrophobic diamine hydrocarbon linking chains with the PMA-b-PS hydrophobic core. These findings indicate an easy method to tune micelle structure with multivalent organic counterions. (Abstract shortened by UMI.)

A Cdc48 “Retrochaperone” Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates*

PubMed Central

Neal, Sonya; Mak, Raymond; Bennett, Eric J.; Hampton, Randolph

2017-01-01

A surprising feature of endoplasmic reticulum (ER)-associated degradation (ERAD) is the movement, or retrotranslocation, of ubiquitinated substrates from the ER lumen or membrane to the cytosol where they are degraded by the 26S proteasome. Multispanning ER membrane proteins, called ERAD-M substrates, are retrotranslocated to the cytosol as full-length intermediates during ERAD, and we have investigated how they maintain substrate solubility. Using an in vivo assay, we show that retrotranslocated ERAD-M substrates are moved to the cytoplasm as part of the normal ERAD pathway, where they are part of a solely proteinaceous complex. Using proteomics and direct biochemical confirmation, we found that Cdc48 serves as a critical “retrochaperone” for these ERAD-M substrates. Cdc48 binding to retrotranslocated, ubiquitinated ERAD-M substrates is required for their solubility; removal of the polyubiquitin chains or competition for binding by addition of free polyubiquitin liberated Cdc48 from retrotranslocated proteins and rendered them insoluble. All components of the canonical Cdc48 complex Cdc48-Npl4-Ufd1 were present in solubilized ERAD-M substrates. This function of the complex was observed for both HRD and DOA pathway substrates. Thus, in addition to the long known ATP-dependent extraction of ERAD substrates during retrotranslocation, the Cdc48 complex is generally and critically needed for the solubility of retrotranslocated ERAD-M intermediates. PMID:28077573

A Cdc48 "Retrochaperone" Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates.

PubMed

Neal, Sonya; Mak, Raymond; Bennett, Eric J; Hampton, Randolph

2017-02-24

A surprising feature of endoplasmic reticulum (ER)-associated degradation (ERAD) is the movement, or retrotranslocation, of ubiquitinated substrates from the ER lumen or membrane to the cytosol where they are degraded by the 26S proteasome. Multispanning ER membrane proteins, called ERAD-M substrates, are retrotranslocated to the cytosol as full-length intermediates during ERAD, and we have investigated how they maintain substrate solubility. Using an in vivo assay, we show that retrotranslocated ERAD-M substrates are moved to the cytoplasm as part of the normal ERAD pathway, where they are part of a solely proteinaceous complex. Using proteomics and direct biochemical confirmation, we found that Cdc48 serves as a critical "retrochaperone" for these ERAD-M substrates. Cdc48 binding to retrotranslocated, ubiquitinated ERAD-M substrates is required for their solubility; removal of the polyubiquitin chains or competition for binding by addition of free polyubiquitin liberated Cdc48 from retrotranslocated proteins and rendered them insoluble. All components of the canonical Cdc48 complex Cdc48-Npl4-Ufd1 were present in solubilized ERAD-M substrates. This function of the complex was observed for both HRD and DOA pathway substrates. Thus, in addition to the long known ATP-dependent extraction of ERAD substrates during retrotranslocation, the Cdc48 complex is generally and critically needed for the solubility of retrotranslocated ERAD-M intermediates. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids

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

Goblirsch, BR; Frias, JA; Wackett, LP

2012-05-22

OleA is a thiolase superfamily enzyme that has been shown to catalyze the condensation of two long-chain fatty acylcoenzyme A (CoA) substrates. The enzyme is part of a larger gene cluster responsible for generating long-chain olefin products, a potential biofuel precursor. In thiolase superfamily enzymes, catalysis is achieved via a ping-pong mechanism. The first substrate forms a covalent intermediate with an active site cysteine that is followed by reaction with the second substrate. For OleA, this conjugation proceeds by a nondecarboxylative Claisen condensation. The OleA from Xanthomonas campestris has been crystallized and its structure determined, along with inhibitor-bound and xenon-derivatizedmore » structures, to improve our understanding of substrate positioning in the context of enzyme turnover. OleA is the first characterized thiolase superfamily member that has two long-chain alkyl substrates that need to be bound simultaneously and therefore uniquely requires an additional alkyl binding channel. The location of the fatty acid biosynthesis inhibitor, cerulenin, that possesses an alkyl chain length in the range of known OleA substrates, in conjunction with a single xenon binding site, leads to the putative assignment of this novel alkyl binding channel. Structural overlays between the OleA homologues, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase and the fatty acid biosynthesis enzyme FabH, allow assignment of the two remaining channels: one for the thioester-containing pantetheinate arm and the second for the alkyl group of one substrate. A short beta-hairpin region is ordered in only one of the crystal forms, and that may suggest open and closed states relevant for substrate binding. Cys143 is the conserved catalytic cysteine within the superfamily, and the site of alkylation by cerulenin. The alkylated structure suggests that a glutamic acid residue (Glu117 beta) likely promotes Claisen condensation by acting as the catalytic base. Unexpectedly, Glu117 beta comes from the other monomer of the physiological dimer.« less

Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids

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

Goblirsch, Brandon R.; Frias, Janice A.; Wackett, Lawrence P.

2012-10-25

OleA is a thiolase superfamily enzyme that has been shown to catalyze the condensation of two long-chain fatty acyl-coenzyme A (CoA) substrates. The enzyme is part of a larger gene cluster responsible for generating long-chain olefin products, a potential biofuel precursor. In thiolase superfamily enzymes, catalysis is achieved via a ping-pong mechanism. The first substrate forms a covalent intermediate with an active site cysteine that is followed by reaction with the second substrate. For OleA, this conjugation proceeds by a nondecarboxylative Claisen condensation. The OleA from Xanthomonas campestris has been crystallized and its structure determined, along with inhibitor-bound and xenon-derivatizedmore » structures, to improve our understanding of substrate positioning in the context of enzyme turnover. OleA is the first characterized thiolase superfamily member that has two long-chain alkyl substrates that need to be bound simultaneously and therefore uniquely requires an additional alkyl binding channel. The location of the fatty acid biosynthesis inhibitor, cerulenin, that possesses an alkyl chain length in the range of known OleA substrates, in conjunction with a single xenon binding site, leads to the putative assignment of this novel alkyl binding channel. Structural overlays between the OleA homologues, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase and the fatty acid biosynthesis enzyme FabH, allow assignment of the two remaining channels: one for the thioester-containing pantetheinate arm and the second for the alkyl group of one substrate. A short {beta}-hairpin region is ordered in only one of the crystal forms, and that may suggest open and closed states relevant for substrate binding. Cys143 is the conserved catalytic cysteine within the superfamily, and the site of alkylation by cerulenin. The alkylated structure suggests that a glutamic acid residue (Glu117{beta}) likely promotes Claisen condensation by acting as the catalytic base. Unexpectedly, Glu117{beta} comes from the other monomer of the physiological dimer.« less

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.

Defining Genome Project Standards in a New Era of Sequencing

ScienceCinema

Chain, Patrick

2018-01-16

Patrick Chain of the DOE Joint Genome Institute gives a talk on behalf of the International Genome Sequencing Standards Consortium on the need for intermediate genome classifications between "draft" and "finished".

Natural product biosynthesis: Tackling tunicamycin

NASA Astrophysics Data System (ADS)

Goddard-Borger, Ethan D.; Withers, Stephen G.

2012-07-01

The tunicamycins, secondary metabolites of various Streptomyces species, are invaluable tools in glycobiology. It has now been shown that their biosynthesis involves an unusual exo-glycal intermediate produced by previously unknown short-chain dehydrogenase/reductase activity.

Electron transport chain-dependent and -independent mechanisms of mitochondrial H2O2 emission during long-chain fatty acid oxidation.

PubMed

Seifert, Erin L; Estey, Carmen; Xuan, Jian Y; Harper, Mary-Ellen

2010-02-19

Oxidative stress in skeletal muscle is a hallmark of various pathophysiologic states that also feature increased reliance on long-chain fatty acid (LCFA) substrate, such as insulin resistance and exercise. However, little is known about the mechanistic basis of the LCFA-induced reactive oxygen species (ROS) burden in intact mitochondria, and elucidation of this mechanistic basis was the goal of this study. Specific aims were to determine the extent to which LCFA catabolism is associated with ROS production and to gain mechanistic insights into the associated ROS production. Because intermediates and by-products of LCFA catabolism may interfere with antioxidant mechanisms, we predicted that ROS formation during LCFA catabolism reflects a complex process involving multiple sites of ROS production as well as modified mitochondrial function. Thus, we utilized several complementary approaches to probe the underlying mechanism(s). Using skeletal muscle mitochondria, our findings indicate that even a low supply of LCFA is associated with ROS formation in excess of that generated by NADH-linked substrates. Moreover, ROS production was evident across the physiologic range of membrane potential and was relatively insensitive to membrane potential changes. Determinations of topology and membrane potential as well as use of inhibitors revealed complex III and the electron transfer flavoprotein (ETF) and ETF-oxidoreductase, as likely sites of ROS production. Finally, ROS production was sensitive to matrix levels of LCFA catabolic intermediates, indicating that mitochondrial export of LCFA catabolic intermediates can play a role in determining ROS levels.

Total Syntheses of (±)-Ovalicin, C4(S*)-Isomer, and Its C5-Analogs and Anti-trypanosomal Activities∥

PubMed Central

Hua, Duy H.; Zhao, Huiping; Battina, Srinivas K.; Lou, Kaiyan; Jimenez, Ana L.; Desper, John; Perchellet, Elisabeth M.; Perchellet, Jean-Pierre H.; Chiang, Peter K.

2008-01-01

Total syntheses of (±)-ovalicin, its C4(S*)-isomer 44, and C5-side chain intermediate 46 were accomplished via an intramolecular Heck reaction of (Z)-3-(t-butyldimethylsilyloxy)-1-iodo-1,6-heptadiene and a catalytic amount of palladium acetate. Subsequent epoxidation, dihydroxylation, methylation and oxidation led to (3S*,5R*,6R*)-5-methoxy-6-(t-butyldimethylsilyloxy)-1-oxaspiro[2.5]octan-4-one (2), a reported intermediate. The addition of a side chain with cis-1-lithio-1,5-dimethyl-1,4-hexadiene (27) followed by oxidation afforded (±)-ovalicin. The functional group manipulation afforded a number of regio- and stereoisomers, which allow the synthesis of analogs for bioevaluation. The structure of 44 was firmly established via a single-crystal X-ray analysis. The stereochemistry at C4 generated from the addition reactions of alkenyllithium with ketones 2, 40, and 45 is dictated by C6-alkoxy functionality. Anti-trypanosomal activities of various ovalicin analogs and synthetic intermediates were evaluated, and C5-side chain analog, 46, shows the strongest activity. Compound 44 shows antiproliferative effect against HL-60 tumor cells in vitro. Compounds 46 and a precursor, (3S*,4R*,5R*,6R*)-5-methoxy-4-[(E)-1’,5’-dimethylhexa-1’,4’–dienyl)]-6-(t-butyldimethylsilyloxy)-1-oxaspiro[2.5]octan-4-ol (28), may be explored for the development of anti-parasitic drugs. PMID:18356059

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.

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.

Drainage fracture networks in elastic solids with internal fluid generation

NASA Astrophysics Data System (ADS)

Kobchenko, Maya; Hafver, Andreas; Jettestuen, Espen; Galland, Olivier; Renard, François; Meakin, Paul; Jamtveit, Bjørn; Dysthe, Dag K.

2013-06-01

Experiments in which CO2 gas was generated by the yeast fermentation of sugar in an elastic layer of gelatine gel confined between two glass plates are described and analyzed theoretically. The CO2 gas pressure causes the gel layer to fracture. The gas produced is drained on short length scales by diffusion and on long length scales by flow in a fracture network, which has topological properties that are intermediate between river networks and hierarchical-fracture networks. A simple model for the experimental system with two parameters that characterize the disorder and the intermediate (river-fracture) topology of the network was developed and the results of the model were compared with the experimental results.

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

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.

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

Stevens, Mark J.; Saleh, Omar A.

We calculated the force-extension curves for a flexible polyelectrolyte chain with varying charge separations by performing Monte Carlo simulations of a 5000 bead chain using a screened Coulomb interaction. At all charge separations, the force-extension curves exhibit a Pincus-like scaling regime at intermediate forces and a logarithmic regime at large forces. As the charge separation increases, the Pincus regime shifts to a larger range of forces and the logarithmic regime starts are larger forces. We also found that force-extension curve for the corresponding neutral chain has a logarithmic regime. Decreasing the diameter of bead in the neutral chain simulations removedmore » the logarithmic regime, and the force-extension curve tends to the freely jointed chain limit. In conclusion, this result shows that only excluded volume is required for the high force logarithmic regime to occur.« less

An informational transition in conditioned Markov chains: Applied to genetics and evolution.

PubMed

Zhao, Lei; Lascoux, Martin; Waxman, David

2016-08-07

In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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.

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.

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.

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…

The Mechanism of Viral Replication. Structure of Replication Complexes of Encephalomyocarditis Virus

PubMed Central

Thach, Sigrid S.; Dobbertin, Darrell; Lawrence, Charles; Golini, Fred; Thach, Robert E.

1974-01-01

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a “bush” of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA. Images PMID:4366773

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

Evidence for an intermediate in tau filament formation.

PubMed

Chirita, Carmen N; Kuret, Jeff

2004-02-17

Alzheimer's disease is defined in part by the intraneuronal accumulation of filaments comprised of the microtubule-associated protein tau. In vitro, fibrillization of full-length, unphosphorylated recombinant tau can be induced under near-physiological conditions by treatment with various agents, including anionic surfactants. Here we examine the pathway through which anionic surfactants promote tau fibrillization using a combination of electron microscopy and fluorescence spectroscopy. Protein and surfactant first interacted in solution to form micelles, which then provided negatively charged surfaces that accumulated tau aggregates. Surface aggregation of tau protein was followed by the time-dependent appearance of a thioflavin S reactive intermediate that accumulated over a period of hours. The intermediate was unstable in the absence of anionic surfaces, suggesting it was not filamentous. Fibrillization proceeded after intermediate formation with classic nucleation-dependent kinetics, consisting of lag phase followed by the exponential increase in filament lengths, followed by an equilibrium phase reached in approximately 24 h. The pathway did not require protein insertion into the micelle hydrophobic core or conformational change arising from mixed micelle formation, because anionic microspheres constructed from impermeable polystyrene were capable of qualitatively reproducing all aspects of the fibrillization reaction. It is proposed that the progression from amorphous aggregation through intermediate formation and fibrillization may underlie the activity of other inducers such as hyperphosphorylation and may be operative in vivo.

Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER

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

Grierson, B. A.; Staebler, G. M.; Solomon, W. M.

Multi-scale fluctuations measured by turbulence diagnostics spanning long and short wavelength spatial scales impact energy confinement and the scale-lengths of plasma kinetic profiles in the DIII-D ITER baseline scenario with direct electron heating. Contrasting discharge phases with ECH + neutral beam injection (NBI) and NBI only at similar rotation reveal higher energy confinement and lower fluctuations when only NBI heating is used. Modeling of the core transport with TGYRO using the TGLF turbulent transport model and NEO neoclassical transport reproduces the experimental profile changes upon application of direct electron heating and indicates that multi-scale transport mechanisms are responsible for changesmore » in the temperature and density profiles. Intermediate and high-k fluctuations appear responsible for the enhanced electron thermal flux, and intermediate-k electron modes produce an inward particle pinch that increases the inverse density scale length. Projection to ITER is performed with TGLF and indicates a density profile that has a finite scale length due to intermediate-k electron modes at low collisionality and increases the fusion gain. Finally, for a range of E×B shear, the dominant mechanism that increases fusion performance is suppression of outward low-k particle flux and increased density peaking.« less

Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER

DOE PAGES

Grierson, B. A.; Staebler, G. M.; Solomon, W. M.; ...

2018-02-01

Multi-scale fluctuations measured by turbulence diagnostics spanning long and short wavelength spatial scales impact energy confinement and the scale-lengths of plasma kinetic profiles in the DIII-D ITER baseline scenario with direct electron heating. Contrasting discharge phases with ECH + neutral beam injection (NBI) and NBI only at similar rotation reveal higher energy confinement and lower fluctuations when only NBI heating is used. Modeling of the core transport with TGYRO using the TGLF turbulent transport model and NEO neoclassical transport reproduces the experimental profile changes upon application of direct electron heating and indicates that multi-scale transport mechanisms are responsible for changesmore » in the temperature and density profiles. Intermediate and high-k fluctuations appear responsible for the enhanced electron thermal flux, and intermediate-k electron modes produce an inward particle pinch that increases the inverse density scale length. Projection to ITER is performed with TGLF and indicates a density profile that has a finite scale length due to intermediate-k electron modes at low collisionality and increases the fusion gain. Finally, for a range of E×B shear, the dominant mechanism that increases fusion performance is suppression of outward low-k particle flux and increased density peaking.« less

Multi-scale transport in the DIII-D ITER baseline scenario with direct electron heating and projection to ITER

NASA Astrophysics Data System (ADS)

Grierson, B. A.; Staebler, G. M.; Solomon, W. M.; McKee, G. R.; Holland, C.; Austin, M.; Marinoni, A.; Schmitz, L.; Pinsker, R. I.; DIII-D Team

2018-02-01

Multi-scale fluctuations measured by turbulence diagnostics spanning long and short wavelength spatial scales impact energy confinement and the scale-lengths of plasma kinetic profiles in the DIII-D ITER baseline scenario with direct electron heating. Contrasting discharge phases with ECH + neutral beam injection (NBI) and NBI only at similar rotation reveal higher energy confinement and lower fluctuations when only NBI heating is used. Modeling of the core transport with TGYRO using the TGLF turbulent transport model and NEO neoclassical transport reproduces the experimental profile changes upon application of direct electron heating and indicates that multi-scale transport mechanisms are responsible for changes in the temperature and density profiles. Intermediate and high-k fluctuations appear responsible for the enhanced electron thermal flux, and intermediate-k electron modes produce an inward particle pinch that increases the inverse density scale length. Projection to ITER is performed with TGLF and indicates a density profile that has a finite scale length due to intermediate-k electron modes at low collisionality and increases the fusion gain. For a range of E × B shear, the dominant mechanism that increases fusion performance is suppression of outward low-k particle flux and increased density peaking.

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.

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.

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.

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.

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.

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.

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

PubMed Central

Rosen, Laura E.; Connell, Katelyn B.; Marqusee, Susan

2014-01-01

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates. PMID:25258414

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

PubMed

Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

2014-10-14

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

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.

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.

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.

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.

An exploration in mineral supply chain mapping using tantalum as an example

USGS Publications Warehouse

Soto-Viruet, Yadira; Menzie, W. David; Papp, John F.; Yager, Thomas R.

2013-01-01

This report uses the supply chain of tantalum (Ta) to investigate the complexity of mineral and metal supply chains in general and show how they can be mapped. A supply chain is made up of all the manufacturers, suppliers, information networks, and so forth, that provide the materials and parts that go into making up a final product. The mineral portion of the supply chain begins with mineral material in the ground (the ore deposit); extends through a series of processes that include mining, beneficiation, processing (smelting and refining), semimanufacture, and manufacture; and continues through transformation of the mineral ore into concentrates, refined mineral commodities, intermediate forms (such as metals and alloys), component parts, and, finally, complex products. This study analyses the supply chain of tantalum beginning with minerals in the ground to many of the final goods that contain tantalum.

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

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.

Anisotropy of the monomer random walk in a polymer melt: local-order and connectivity effects

NASA Astrophysics Data System (ADS)

Bernini, S.; Leporini, D.

2016-05-01

The random walk of a bonded monomer in a polymer melt is anisotropic due to local order and bond connectivity. We investigate both effects by molecular-dynamics simulations on melts of fully-flexible linear chains ranging from dimers (M  =  2) up to entangled polymers (M  =  200). The corresponding atomic liquid is also considered a reference system. To disentangle the influence of the local geometry and the bond arrangements, and to reveal their interplay, we define suitable measures of the anisotropy emphasising either the former or the latter aspect. Connectivity anisotropy, as measured by the correlation between the initial bond orientation and the direction of the subsequent monomer displacement, shows a slight enhancement due to the local order at times shorter than the structural relaxation time. At intermediate times—when the monomer displacement is comparable to the bond length—a pronounced peak and then decays slowly as t -1/2, becoming negligible when the displacement is as large as about five bond lengths, i.e. about four monomer diameters or three Kuhn lengths. Local-geometry anisotropy, as measured by the correlation between the initial orientation of a characteristic axis of the Voronoi cell and the subsequent monomer dynamics, is affected at shorter times than the structural relaxation time by the cage shape with antagonistic disturbance by the connectivity. Differently, at longer times, the connectivity favours the persistence of the local-geometry anisotropy, which vanishes when the monomer displacement exceeds the bond length. Our results strongly suggest that the sole consideration of the local order is not enough to understand the microscopic origin of the rattling amplitude of the trapped monomer in the cage of the neighbours.

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.

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.

Productivity, disturbance and ecosystem size have no influence on food chain length in seasonally connected rivers.

PubMed

Warfe, Danielle M; Jardine, Timothy D; Pettit, Neil E; Hamilton, Stephen K; Pusey, Bradley J; Bunn, Stuart E; Davies, Peter M; Douglas, Michael M

2013-01-01

The food web is one of the oldest and most central organising concepts in ecology and for decades, food chain length has been hypothesised to be controlled by productivity, disturbance, and/or ecosystem size; each of which may be mediated by the functional trophic role of the top predator. We characterised aquatic food webs using carbon and nitrogen stable isotopes from 66 river and floodplain sites across the wet-dry tropics of northern Australia to determine the relative importance of productivity (indicated by nutrient concentrations), disturbance (indicated by hydrological isolation) and ecosystem size, and how they may be affected by food web architecture. We show that variation in food chain length was unrelated to these classic environmental determinants, and unrelated to the trophic role of the top predator. This finding is a striking exception to the literature and is the first published example of food chain length being unaffected by any of these determinants. We suggest the distinctive seasonal hydrology of northern Australia allows the movement of fish predators, linking isolated food webs and potentially creating a regional food web that overrides local effects of productivity, disturbance and ecosystem size. This finding supports ecological theory suggesting that mobile consumers promote more stable food webs. It also illustrates how food webs, and energy transfer, may function in the absence of the human modifications to landscape hydrological connectivity that are ubiquitous in more populated regions.

Productivity, Disturbance and Ecosystem Size Have No Influence on Food Chain Length in Seasonally Connected Rivers

PubMed Central

Warfe, Danielle M.; Jardine, Timothy D.; Pettit, Neil E.; Hamilton, Stephen K.; Pusey, Bradley J.; Bunn, Stuart E.; Davies, Peter M.; Douglas, Michael M.

2013-01-01

The food web is one of the oldest and most central organising concepts in ecology and for decades, food chain length has been hypothesised to be controlled by productivity, disturbance, and/or ecosystem size; each of which may be mediated by the functional trophic role of the top predator. We characterised aquatic food webs using carbon and nitrogen stable isotopes from 66 river and floodplain sites across the wet-dry tropics of northern Australia to determine the relative importance of productivity (indicated by nutrient concentrations), disturbance (indicated by hydrological isolation) and ecosystem size, and how they may be affected by food web architecture. We show that variation in food chain length was unrelated to these classic environmental determinants, and unrelated to the trophic role of the top predator. This finding is a striking exception to the literature and is the first published example of food chain length being unaffected by any of these determinants. We suggest the distinctive seasonal hydrology of northern Australia allows the movement of fish predators, linking isolated food webs and potentially creating a regional food web that overrides local effects of productivity, disturbance and ecosystem size. This finding supports ecological theory suggesting that mobile consumers promote more stable food webs. It also illustrates how food webs, and energy transfer, may function in the absence of the human modifications to landscape hydrological connectivity that are ubiquitous in more populated regions. PMID:23776641

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

Genetic Diversity of Plasmodium falciparum Merozoite Surface Protein-1 Block 2 in Sites of Contrasting Altitudes and Malaria Endemicities in the Mount Cameroon Region

PubMed Central

Wanji, Samuel; Kengne-Ouafo, Arnaud J.; Joan Eyong, Ebanga E.; Kimbi, Helen K.; Tendongfor, Nicholas; Ndamukong-Nyanga, Judith L.; Nana-Djeunga, Hugues C.; Bourguinat, Catherine; Sofeu-Feugaing, David D.; Charvet, Claude L.

2012-01-01

The present study analyzed the relationship between the genetic diversity of Plasmodium falciparum and parasitologic/entomologic indices in the Mount Cameroon region by using merozoite surface protein 1 as a genetic marker. Blood samples were collected from asymptomatic children from three altitude zones (high, intermediate, and low). Parasitologic and entomologic indices were determined by microscopy and landing catch mosquito collection/circumsporozoite protein–enzyme-linked immunosorbent assay, respectively. A total of 142 randomly selected P. falciparum-positive blood samples were genotyped by using a nested polymerase chain reaction–based technique. K-1 polymerase chain reaction products were also sequenced. As opposed to high altitude, the highest malaria prevalence (70.65%) and entomologic inoculation rate (2.43 infective/bites/night) were recorded at a low altitude site. Seven (18.91%), 22 (36.66%), and 19 (42.22%) samples from high, intermediate, and low altitudes, respectively, contained multiclonal infections. A new K-1 polymorphism was identified. This study shows a positive non-linear association between low/intermediate altitude (high malaria transmission) and an increase in P. falciparum merozoite surface protein 1 block 2 polymorphisms. PMID:22556072

Genetic diversity of Plasmodium falciparum merozoite surface protein-1 block 2 in sites of contrasting altitudes and malaria endemicities in the Mount Cameroon region.

PubMed

Wanji, Samuel; Kengne-Ouafo, Arnaud J; Eyong, Ebanga E Joan; Kimbi, Helen K; Tendongfor, Nicholas; Ndamukong-Nyanga, Judith L; Nana-Djeunga, Hugues C; Bourguinat, Catherine; Sofeu-Feugaing, David D; Charvet, Claude L

2012-05-01

The present study analyzed the relationship between the genetic diversity of Plasmodium falciparum and parasitologic/entomologic indices in the Mount Cameroon region by using merozoite surface protein 1 as a genetic marker. Blood samples were collected from asymptomatic children from three altitude zones (high, intermediate, and low). Parasitologic and entomologic indices were determined by microscopy and landing catch mosquito collection/circumsporozoite protein-enzyme-linked immunosorbent assay, respectively. A total of 142 randomly selected P. falciparum-positive blood samples were genotyped by using a nested polymerase chain reaction-based technique. K-1 polymerase chain reaction products were also sequenced. As opposed to high altitude, the highest malaria prevalence (70.65%) and entomologic inoculation rate (2.43 infective/bites/night) were recorded at a low altitude site. Seven (18.91%), 22 (36.66%), and 19 (42.22%) samples from high, intermediate, and low altitudes, respectively, contained multiclonal infections. A new K-1 polymorphism was identified. This study shows a positive non-linear association between low/intermediate altitude (high malaria transmission) and an increase in P. falciparum merozoite surface protein 1 block 2 polymorphisms.

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 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.

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

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.

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.

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