The Rheology of Liquid Pentane Isomers by Non-Equilibrium Molecular Dynamics Simulations

Abstract

In this paper, non-equilibrium molecular dynamics (NEMD) simulations of planar Couette flow are reported for an expanded collapsed atom model for liquid pentane isomers at 273.15 K. The strain rate dependent viscosity for liquid pentane isomers exhibits shear-thinning and a linear dependence on γ^1/2. Newtonian viscosities for liquid pentane isomers obtained by a linear extrapolation to zero strain rate are: 0.256cP for normal pentane, 0.219cP for isopentane, and 0.168cP for neopentane. The strain rate dependent pressure difference and normal stress difference vary nearly linearly with the γ^3/2 law and the γ law, respectively, for all three liquid pentane isomers. The overall trend of the square of radius of gyration and end-to-end distance for normal pentane is a linear increase with strain rate. For isopentane, the trend hardly changes for the range of shear rate in this study. The alignment angle decreases with increasing strain rate and the alignment angle of the straight chain alkane is less than that of the branched chain alkane. The average percentage of C?C?C?C trans for normal pentane as a function of strain rate is in excellent correlation with the square of the radius of gyration and the average end-to-end distance. Applying the strain rate in the x-direction, the alignment angle is forced to decrease and the percentage of C?C?C?C trans increases with increasing strain rate.     

Isolation and Identification of n-Butane-assimilating Bacterium

A bacterial strain capable of assimilating gaseous n-alkanes was newly isolated from activated sludge by enrichment culture technique using n-butane as the sole carbon source. The strain was identified as Pseudomonas butanovora sp. nov. It utilised n-alkanes of C₂~C₉, primary alcohols and carboxylic acids for growth, but did not utilize sugars and C₁ compounds. The cell yields on gaseous n-alkanes, such as ethane, propane and n-butane, were 80% or more. The maximum specific growth rate on n-butane was 0.22 hr^?1 at 30°C, pH 7.0. Dried cells of this new isolate grown on n-butane contained 73% pure protein.     

Growth of <Emphasis Type="Italic">Pseudomonas chloritidismutans</Emphasis> AW-1<Superscript>T</Superscript> on <Emphasis Type="Italic">n</Emphasis>-alkanes with chlorate as electron acceptor

Microbial (per)chlorate reduction is a unique process in which molecular oxygen is formed during the dismutation of chlorite. The oxygen thus formed may be used to degrade hydrocarbons by means of oxygenases under seemingly anoxic conditions. Up to now, no bacterium has been described that grows on aliphatic hydrocarbons with chlorate. Here, we report that Pseudomonas chloritidismutans AW-1^T grows on n-alkanes (ranging from C7 until C12) with chlorate as electron acceptor. Strain AW-1^T also grows on the intermediates of the presumed n-alkane degradation pathway. The specific growth rates on n-decane and chlorate and n-decane and oxygen were 0.5 ± 0.1 and 0.4 ± 0.02 day⁻¹, respectively. The key enzymes chlorate reductase and chlorite dismutase were assayed and found to be present. The oxygen-dependent alkane oxidation was demonstrated in whole-cell suspensions. The strain degrades n-alkanes with oxygen and chlorate but not with nitrate, thus suggesting that the strain employs oxygenase-dependent pathways for the breakdown of n-alkanes.     

Microbial oxidation of hydrocarbons measured by oxygraphy

Summary The Clark oxygen electrode was used to measure the microbial oxidation of hydrocarbons using preparations of resting cell suspensions. A strain of Corynebacterium sp. (7E1C) which utilized n-octane as sole carbon and energy source was examined for its ability to oxidize a variety of hydrocarbon substrates. The oxidation by resting cells exhibited an optimal temperature of 30° and an optimal pH range of 7.0–7.6. 1-Octanol, octanal, and octanoic acid were oxidized at rates comparable to n-octane. With the exception of n-decane, n-alkanes from pentane through heptadecane were attacked with a progressive increase in specific activity up the homologous series to n-octane, followed by a decrease as the hydrocarbon chain became progressively longer. n-Alkenes and halogenated n-alkanes substituted in the one position were oxidized at appreciably lower rates than the corresponding n-alkanes. Iso-Alkanes, cyclo-alkanes and aromatic hydrocarbons were relatively unsusceptible to oxidative attack.     

The substrate specificity of two yeast strains utilizing hydrocarbons

StrainsCandida lipolytica 4-1 andCandida lipolytica K were compared in their growth and dawaxing capacities during batch growth on model gas oil. The model gas oil was composed of a mixture of even-numbered puren-alkanes (n-decane ton-dotriacontane) dissolved in dewaxed gas oil. The results show that both strains differ in their substrate specificity and in the sequence of utilization of individualn-alkanes. Strain K, previously used for dewaxing of mineral oil, has its substrate specificity shifted toward the highern-alkanes.     

Effects of biosurfactants produced by Candida antarctica on the biodegradation of petroleum compounds

The effects of biosurfactants on the biodegradation of petroleum compounds were investigated. Candida antarctica T-34 could produce extracellular biosurfactant mannosylerythritol lipids (MELs) when it was cultured in vegetable oil. In addition, in our previous study, it was found that this strain could also produce a new type of biosurfactant while it grew on n-undecane (C₁₁H₂₄), and the biosurfactant was named as BS-UC. In flask culture of Candida antarctica, the addition of BS-UC could improve the biodegradation rate of some n-alkanes (e.g. 90.2% for n-decane, 90.2% for n-undecane, 89.0% for dodecane), a mixture of n-alkanes (82.3%) and kerosene (72.5%). By comparing the effects of the biosurfactants BS-UC and MEL and chemical surfactants on the biodegradation of crude oil, it was found that biosurfactants could be used to enhance the degradation of petroleum compounds instead of chemical surfactants. In a laboratory scale immobilized bioreactor, the addition of biosurfactant improved not only the emulsification of kerosene in simulated wastewater but also its biodegradation rate. The highest degradation rate of kerosene by addition of MEL and BS-UC reached 87 and 90% at 15 h, respectively. The results showed that the biosurfactant BS-UC was highly promising for work on biodegradation of hydrophobic contaminants.     

The uptake of n-alkanes from alkane mixtures during growth of the hydrocarbon-utilizing fungus Cladosporium resinae

Summary Cladosporium resinae growing on alkane mixtures removed n-alkanes sequentially in order of increasing molecular weight, each at about the same rate as during growth on it as single alkane. This sequence is not in order of the ability of each alkane to support growth. No alkane-specific extracellular solubilizing agent able to affect the order o metabolism could be detected during the growth of C. resinae on mixed n-alkanes, but supplementing the medium with phospholipids like those produced during growth on specific alkanes increased the rate or removal of the respective alkanes. Kinetic analysis indicated that the uptake of dodecane, hexadecane and octadecane from a mixture could be by a common mechanism, the order being determined, through competition, by the affinity of the system for each alkane.     

Characterization of 2T engine oil degrading indigenous bacteria,isolated from high altitude (Mussoorie), India

The biodegradability of petroleum hydrocarbons such as polycyclic aromatic hydrocarbons (PAHs) and n-branched alkanes etc. of 2T engine oil were studied in aqueous media using bacterial strain isolated from petroleum contaminated soil of high altitude. Out of five petroleum degrading bacterial strain one of the most growing bacteria was identified as Enterobacter strain by morphological, physiological, biochemical and partial sequencing of 16S rDNA. This strain was capable of degrading 75 ± 3% of n-alkanes, 32 ± 5% PAHs, and the abiotic loss was 24 ± 6% during 10 days incubation period. 85 ± 2% of n-alkanes and 51 ± 3% PAHs were biodegraded in 20 days. The abiotic loss during this period was 15 ± 3%. In 30 days of incubation period 98% ± 1% n-alkanes and 75 ± 3% PAHs were degraded. As expected abiotic losses were smaller with increasing long chain alkanes and PAH’s concentration. An increment in oil degradation was correlated to an increase in cell number indicating that the bacterial isolate was responsible for the oil degradation. The hydrocarbon contents were measured by Shimadzu QP-2000 Gas chromatography/mass spectrometry by ULBON HR-1 column.     

Uptake of volatilen-alkanes byPseudomonas PG-I

Using a bacterial speciesPseudomonas PG-1, evidence has been obtained which indicates that uptake ofn-pentane ton-octane by microbial cells takes place primarily from the gas phase either directly orvia the aqueous phase. Specific growth rate increased along with the increase in substrate concentration but above the alkane concentration of 0.3% by volume, specific growth rate decreased indicating substrate inhibition of growth. In the case of less volatile alkanes,n-nonane andn-decane, substrate transfer is predominantly through substrate solubilization system elaborated by the cells. EDTA, a strong inhibitor of hydrocarbon solubilization by the cells, inhibited growth on these two alkanes but had negligible effect on growth onn-pentane ton-octane.     

Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria

The capacity of denitrifying bacteria for anaerobic utilization of saturated hydrocarbons (alkanes) was investigated with n-alkanes of various chain lengths and with crude oil in enrichment cultures containing nitrate as electron acceptor. Three distinct types of denitrifying bacteria were isolated in pure culture. A strain (HxN1) with oval-shaped, nonmotile cells originated from a denitrifying enrichment culture with crude oil and was isolated with n-hexane (C₆H₁₄). Another strain (OcN1) with slender, rod-shaped, motile cells was isolated from an enrichment culture with n-octane (C₈H₁₈). A third strain (HdN1) with oval, somewhat pleomorphic, partly motile cells originated from an enrichment culture with aliphatic mineral oil and was isolated with n-hexadecane (C₁₆H₃₄). Cells of hexane-utilizing strain HxN1 grew homogeneously in the growth medium and did not adhere to the alkane phase, in contrast to the two other strains. Quantification of substrate consumption and cell growth revealed the capacity for complete oxidation of alkanes under strictly anoxic conditions, with nitrate being reduced to dinitrogen. Received: 3 August / Accepted: 6 October 1999     

Production of fatty acids and lipid by a Candida sp. growing on a fraction of n-alkanes predominating in tridecane

A Candida sp. was grown on a fraction of n-alkanes (dodecane 22%, tridecane 48%, tetradecane 28%) as sole carbon source. The growth rate was increased most markedly by using high concentrations of n-alkanes (16.7% v/v). When grown in a 5 liter fermentor, the yeast reached its highest yield (60 g. of cell dry wt/l) with a concomitant high yield of fatty acids (21 g of fatty acids/l), by using a nitrogen-deficient medium. To achieve good growth, it was essential to use an inoculum (1 part into 10) of rapidly growing cells and beneficial to increase the agitation rate gradually once growth had begun. After 108 hr maximum conversions of substrate to product were: 71.5% (w/w) for alkanes into cells and 24.8% (w/w) for alkanes into fatty acids. Of the, total fatty acids at the end of the fat-accumulating phase of growth 54% were shorter in chain length than palmitic acid (C₁₆H₃₂O₂). When grown on glucose, as sole carbon source, less than 2% of the total fatty acids were shorter than palmitic acid. When n-alkanes were added to cells growing on glucose, short-chain fatty acids (C₁₀ to C₁₄) were synthesized immediately, indicating a derepressed enzyme system for hydrocarbon assimilation and the absence of diauxie. The production of these acids was at the apparent sacrifice of linoleic acid synthesis. In spite of the high conversion ratios, it is concluded that it would be uneconomical to produce fatty acids, even expensive ones such as lauric acid, by microbial transformation of n-alkanes.     

Disruption of the SCS2 Ortholog in the Alkane-Assimilating Yeast Yarrowia lipolytica Impairs Its Growth on n-Decane,but Does Not Impair Inositol Prototrophy

Disruption of an SCS2 ortholog impaired the growth of the alkane-assimilating yeast Yarrowia lipolytica on n-alkanes, particularly on n-decane, although the mRNA level of the ALK1 gene encoding a highly inducible cytochrome P450ALK was not much affected. The same disruption did not cause inositol auxotrophy, implying that Y. lipolytica SCS2 has a different function from its Saccharomyces cerevisiae counterpart.     

Simulation of Polymer Solutions by Dissipative Particle Dynamics

Abstract

Dissipative Particle Dynamics (DPD) is employed to model the dynamics and rheology of polymer solutions, and suspensions of spherical particles with adsorbed polymers. Static and dynamic scaling relationships for the variation of radius of gyration and relaxation time with polymer chain length are reviewed, demonstrating that the DPD polymer solution model correctly represents the effects of hydrodynamic interaction and excluded volume. Rheological simulations for both polymer solutions and polymer-sphere suspensions predict Newtonian viscosities at low shear rate followed by shear-thinning behavior as a reduced shear rate of unity is approached. Both the Newtonian viscosity and the extent of shear-thinning are greatly enhanced in the case of good solvents, compared to the viscosity curves for polymers and polymer-spheres structures dissolved in theta solvents and poor solvents.     

Bacterial metabolism of long-chain <Emphasis Type="Italic">n</Emphasis>-alkanes

Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.     

A Hypothetical Cyclic Pathway for the Metabolism of Odd-carbon n-Alkanes or Propionyl-CoA via Seven-carbon Tricarboxylic Acids in Yeasts

An extensive study has been undertaken to elucidate the physiological significance of threo-D_s-2-methylisocitric acid produced mainly from odd-carbon n-alkanes by a mutant strain of Candida lipolytica. The mutant strain showed slower growth responses to odd-carbon n-alkanes, especially of shorter chain-length, and failed to utilize this acid as sole carbon source, whereas the parent strain and many other yeasts tested were able to utilize this acid. About one half of yeasts tested accumulated this acid extracellularly. Under a thiamine-deficient condition, amounts of pyruvate produced by the parent strain from odd-carbon n-alkanes were ten times as large as those from even-carbon n-alkanes. A scheme for the partial oxidation of propionyl-CoA to pyruvate via C₇-tricarboxylic acid by yeasts was supposed. This scheme may offer suggestion on the metabolism of propionyl-CoA by other living organisms. A hypothetical pathway of citrate accumulation from odd-carbon n-alkane was also presented.     

Isolation and characterization of long-chain alkane–degrading Acinetobacter sp. BT1A from oil-contaminated soil in Diyarbakır,in the Southeast of Turkey

A strain of long-chain alkane–degrading bacteria, BT1A, was isolated from oil-contaminated soil in Diyarbak?r, in the southeast of Turkey. Morphological, biochemical, and physiological characterization and 16S rRNA gene sequence analysis showed that the strain BT1A was a member of Acinetobacter genus, and it was found to be closely related to Acinetobacter baumannii. The strain BT1A was able to utilize crude petroleum as carbon and energy sources in order to grow. Among the aliphatic hydrocarbons, growth was observed only in the medium containing long-chain alkanes (tridecane, pentadecane, and hexadecane) and squalene. Hexadecane was the most preferred hydrocarbon among the long-chain alkanes. Gas chromatography–mass spectrometry (GC-MS) analysis showed that BT1A degraded 83% of n-alkanes of 1% crude oil in 7 days. The present study indicates that the isolated strain can well be used for biodegradation of hydrocarbons in oil-contaminated sites.     

Purified Penicillin Binding Proteins 1Bs from Escherichia coli Membrane Showing Activities of Both Peptidoglycan Polymerase and Peptidoglycan Crosslinking Enzyme

Our biotransformation using Escherichia coli expressing a cytochrome P450 (CYP) belonging to the CYP153A family from Acinetobacter sp. OC4 produced a great amount of 1-octanol (2,250 mg per liter) from n-octane after 24 h of incubation. This level of production is equivalent to the maximum level previously achieved in biotransformation experiments of alkanes. In addition, the initial production rate of 1-octanol was maintained throughout the entire incubation period. These results indicate that we have achieved the functional and stable expression of a CYP in E. coli for the first time. Further, our biotransformation system showed α,ω-diterminal oxidation activity of n-alkanes, and a large amount of 1,8-octanediol (722 mg per liter) was produced from 1-octanol after 24 h of incubation. This is the first report on the bioproduction of α,ω-alkanediols from n-alkanes or 1-alkanols.