| 1. |
- Bazooyar, Faranak, 1972, et al.
(författare)
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Computational studies of water and carbon dioxide interactions with cellobiose
- 2015
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Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 0948-5023 .- 1610-2940. ; 21:1, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- B3LYP/6-311++G** with dispersion correction (DFT-D) was used to study local and global minimum energy structures of water (H2O) or carbon dioxide (CO2) bonding with a pair of cellobiose molecules. The calculations showed that neither the H2O nor the CO2 prefer to be between the cellobiose molecules, and that the minimum energy structures occur when these molecules bond to the outer surface of the cellobiose pair. The calculations also showed that the low energy structures have a larger number of inter-cellobiose hydrogen bonds than the high energy structures. These results indicate that penetration of H2O or CO2 between adjacent cellobiose pairs, which would assist steam or supercritical CO2 (SC-CO2) explosion of cellulose, is not energetically favored. Comparison of the energies obtained with DFT-D and DFT (the same method but without dispersion correction) show that both hydrogen bonds and van der Waals interactions play an important role in cellobiose-cellobiose interactions.
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| 2. |
- Bazooyar, Faranak, et al.
(författare)
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Molecular-level Simulations of Cellulose Dissolution by Steam and SC-CO2 Explosion
- 2014
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Konferensbidrag (refereegranskat)abstract
- Dissolution of cellulose is an important but tough step in biofuel production from lignocellulosic materials. Steam and supercritical carbon dioxide (SC-CO2) explosion are two effective methods for dissolution of some lignocellulosic materials. Loading and explosion are the major processes of these methods. Studies of these processes were performed using grand canonical Monte Carlo and molecular dynamics simulations at different pressure/ temperature conditions on the crystalline structure of cellulose. The COMPASS force field was used for both methods. The validity of the COMPASS force field for the calculations was confirmed by comparing the energy and structures obtained from molecular mechanics simulations of cellobiose (the repeat unit of cellulose), water–cellobiose, water-cellobiose pair and CO2-cellobiose pair systems with those obtained from first principle calculations with and without dispersion correction. A larger disruption of the cellulose crystal structure was seen during loading than that during the explosion process. This is seen by an increased separation of the cellulose chains from the centre of mass of the crystal during the initial stages of the loading, especially for chains in the outer shell of the crystalline structure. Reducing and non-reducing ends of the cellulose crystal show larger disruption than the central core; this leads to increasing susceptibility to enzymatic attack in these end regions. There was also change from the syn to the anti torsion angle conformations, especially for chains in the outer cellulose shell. Increasing the temperature increases the disruption of the crystalline structure during loading and explosion.
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| 3. |
- Bazooyar, Faranak
(författare)
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Molecular-level Simulations of Cellulose Dissolution by Steam and SC-CO2 Explosion
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dissolution of cellulose is an important but complicated step in biofuel production from lignocellulosic materials. Steam and supercritical carbon dioxide (SC-CO2) explosion are two effective methods for dissolution of some lignocellulosic materials. Loading and explosion are the major processes of these methods. Studies of these processes were performed using grand canonical Monte Carlo and molecular dynamics simulations at different pressure/ temperature conditions on the crystalline structure of cellulose. The COMPASS force field was used for both methods. The validity of the COMPASS force field for these calculations was confirmed by comparing the energies and structures obtained from this force field with first principles calculations. The structures that were studied are cellobiose (the repeat unit of cellulose), water–cellobiose, water-cellobiose pair and CO2-cellobiose pair systems. The first principles methods were preliminary based on B3LYP density functional theory with and without dispersion correction. A larger disruption of the cellulose crystal structure was seen during loading than that during the explosion process. This was seen by an increased separation of the cellulose chains from the centre of mass of the crystal during the initial stages of the loading, especially for chains in the outer shell of the crystalline structure. The ends of the cellulose crystal showed larger disruption than the central core; this leads to increasing susceptibility to enzymatic attack in these end regions. There was also change from the syn to the anti torsion angle conformations during steam explosion, especially for chains in the outer cellulose shell. Increasing the temperature increased the disruption of the crystalline structure during loading and explosion.
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| 4. |
- Bazooyar, Faranak, et al.
(författare)
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Molecular-level Simulations of Cellulose Steam Explosion
- 2015
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Ingår i: Quantum Matter. - : American Scientific Publishers. - 2164-7615 .- 2164-7623. ; 4:2, s. 115-122
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Tidskriftsartikel (refereegranskat)abstract
- Grand canonical Monte Carlo and molecular dynamics simulations are used to study steam explosion of crystalline cellulose using 100, 160, 210 and 250 °C saturated steam. The simulations are based on the COMPASS force field, which provides a valid description of the cellulose crystal structure and water-cellobiose interactions. Disruption of the crystal structure during steaming is typically larger than that during the explosion stage and the restructuring is larger at increased temperature and pressure. This is seen by an increased separation of the cellulose chains from the center of mass of the crystal during the initial stages of the steaming, especially for chains in the outer shell of the elementary fibril. There is a large change in the radius of gyration and fraction of anti torsion angle conformers for chains in the outer shell of the elementary fibril. In addition, the disruption at the reducing and non-reducing ends of the cellulose crystal is larger than in the central core, increasing susceptibility to enzymatic attack in these end regions.
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| 5. |
- Bazooyar, Faranak, 1972, et al.
(författare)
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Molecular Modelling of Cellulose Dissolution
- 2013
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Ingår i: Journal of Computational and Theoretical Nanoscience. - : American Scientific Publishers. - 1546-1955 .- 1546-1963. ; 10:11, s. 2639-2646
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Tidskriftsartikel (refereegranskat)abstract
- In this work we present computational studies that shed light on the molecular mechanism of the initial stages of cellulose dissolution in saturated steam, which is an important pretreatment step in the conversion of lignocellulose to biofuel. The COMPASS, Dreiding and Universal molecular mechanics force fields and the B3LYP density functional with 6-311G, 6-311++G(d, p) and 6-311++G(2d, 2p) basis sets were used to study systems containing glucose, cellobiose and water. These molecular systems were studied since they are sufficiently small to perform the density functional theory calculations in a tractable time, while also being relevant to the dissolution of cellulose in saturated steam. Comparison of the energies and structures obtained from the three force fields with those obtained from the first principles method showed that the COMPASS force field is preferred to the other two and that this force field gives similar structures obtained from the first principles method. This supports the validity of the COMPASS force field for studying cellulose dissolution in saturated steam, and preliminary simulations were performed using grand canonical Monte Carlo and molecular dynamics simulations of cellulose dissolution in saturated steam at 100 degrees C and 1 bar, 160 degrees C and 6.2 bar, and 250 degrees C and 39.7 bar. The results show that the cellulose crystal dissolves in saturated steam at the higher temperatures and pressures.
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| 6. |
- Bazooyar, Faranak, 1972, et al.
(författare)
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Validating empirical force fields for molecular-level simulation of cellulose dissolution
- 2012
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Ingår i: Computational and Theoretical Chemistry. - : Elsevier BV. - 2210-271X .- 2210-2728. ; 984, s. 119-127
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Tidskriftsartikel (refereegranskat)abstract
- The calculations presented here, which include dynamics simulations using molecular mechanics force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of these force fields was assessed by comparing structures and energies of cellobiose, which is the shortest cellulose chain, obtained from the force fields with those obtained from MP2 and DFT methods. In agreement with the first principles methods, COMPASS is the only force field of the three studied here that favors the anti form of cellobiose in the vacuum. This force field was also used to compare changes in energies when hydrating cellobiose with 1-4 water molecules. Although the COMPASS force field does not yield the change from anti to syn minimum energy structure when hydrating with h more than two water molecules - as predicted by OFT - it does predict that the syn conformer is preferred when simulating cellobiose in bulk liquid water and at temperatures relevant to cellulose dissolution. This indicates that the COMPASS force field yields valid structures of cellulose under these conditions. Simulations based on the COMPASS force field show that, due to entropic effects, the syn form of cellobiose is energetically preferred at elevated temperature, both in vacuum and in bulk water. This is also in agreement with DFT calculations.
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| 7. |
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| 8. |
- Bolton, Kim, et al.
(författare)
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Beräkningsteknik
- 2009
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Ingår i: Vetenskap för profession. - : Högskolan i Borås. - 1654-6520. - 9789185659494 ; :10, s. 63-68
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 9. |
- Karimi-Avargani, M., et al.
(författare)
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Accelerating degradation of natural rubber latex gloves by a consortium of microorganisms in an agricultural soil sample
- 2024
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Ingår i: International Journal of Environmental Science and Technology. - 1735-1472 .- 1735-2630.
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Tidskriftsartikel (refereegranskat)abstract
- The complexity of the vulcanized rubber makes it difficult to be degraded by microorganisms. It is believed that a microbial consortium can improve the efficiency of the biodegradation process. Fertile soil houses a plethora of microorganisms with innate ability to adapt to various chemical substances come into contact with its texture. Consequently, a soil sample which was in direct contact with tire wastes for more than 13 years was employed in this work to enhance the biodegradation of natural rubber (NR) gloves. The active soil microorganisms associated with the NR latex degradation were isolated and identified using 16S rRNA gene sequencing method. The biodegradation of NR gloves in the soil sample containing these bacteria was investigated and the results represented 87% and 79% weight loss in the examination and surgical gloves after 12 months of treatment, respectively. The total biodegradation was achieved after 13 and 15 months which was nearly half of the reported time in the landfill processes. Thermal gravimetric analysis (TGA) showed 15% incremental weight decrease for the treated samples after three months in comparison with the blanks and the FT-IR spectra approved the breaking of the cross-link sulfur bonds as well as the formation of carbonyl groups which indicated oxidative cleavage of double bonds of the polymer chain. A chemical mechanism for the biodegradation was suggested based on the obtained results to explain the higher efficiency of biodegradation in this work.
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| 10. |
- Karimi-Avargani, Mina, et al.
(författare)
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The promiscuous potential of cellulase in degradation of polylactic acid and its jute composite
- 2021
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Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 278
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Tidskriftsartikel (refereegranskat)abstract
- It has been suggested that cellulolytic enzymes can be effective on the degradation of PLA samples. The idea was investigated by examining the impact of cellulase on degradation of PLA and PLA-jute (64/36) composite in an aqueous medium. The obtained results demonstrated 55% and 61% thickness reduction in PLA and PLA-jute specimens after four months of treatment, respectively. Gel permeation chromatography (GPC) showed significant decline in the number average molecular weight (Mn) approximately equal to 85% and 80% for PLA and PLA-jute in comparison with their control. The poly dispersity index (PDI) of PLA and PLA-jute declined 41% and 49% that disclosed more homogenous distribution in molecular weight of the polymer after treatment with cellulase. The cellulase promiscuity effect on PLA degradation was further revealed by Fourier-transform infrared spectroscopy (FT-IR) analysis where substantial decrease in the peak intensities of the polymer related functional groups were observed. In addition, PLA biodegradation was studied in more detail by differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) of control and cellulase treated specimens. The obtained results confirmed the promiscuous function of cellulase in the presence or the absence of jute as the specific substrate of cellulase. This can be considered as a major breakthrough to develop effective biodegradation processes for PLA products at the end of their life cycle.
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