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Publications (7 of 7) Show all publications
Erdtman, E., Bohlén, M., Ahlström, P., Gkourmpis, T., Berlin, M., Andersson, T. & Bolton, K. (2016). A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites. Journal of Polymer Science Part B: Polymer Physics, 54, 589-602
Open this publication in new window or tab >>A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites
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2016 (English)In: Journal of Polymer Science Part B: Polymer Physics, ISSN 0887-6266, E-ISSN 1099-0488, Vol. 54, p. 589-602Article in journal (Refereed) Published
Abstract [en]

Monte Carlo and molecular dynamics simulations were performed to investigate the effect on the solubility, diffusion, and permeability of water and oxygen when adding graphene or single-walled carbon nanotubes (SWCNTs) to polyethylene (PE). When compared with pure PE, addition of graphene lowered the solubility of water, whereas at lower temperatures, the oxygen solubility increased because of the oxygen–graphene interaction. Addition of SWCNTs lowered the solubility of both water and oxygen when compared with pure PE. A detailed analysis showed that an ordered structure of PE is induced near the additive surface, which leads to a decrease in the diffusion coefficient of both penetrants in this region. The addition of graphene does not change the permeation coefficient of oxygen (in the direction parallel to the filler) and, in fact, may even increase this coefficient when compared with pure PE. In contrast, the water permeability is decreased when graphene is added to PE. The addition of SWCNTs decreases the permeability of both penetrants. Graphene can consequently be added to selectively increase the solubility and permeation of oxygen over water, at least at lower temperatures. 

Keywords
diffusion, molecular modeling, nanocomposites, polyethylene (PE), solubility
National Category
Polymer Chemistry
Research subject
Textiles and Fashion (General)
Identifiers
urn:nbn:se:hb:diva-10816 (URN)10.1002/polb.23951 (DOI)000368942900007 ()2-s2.0-84956976939 (Scopus ID)
Available from: 2016-10-03 Created: 2016-10-03 Last updated: 2018-11-26Bibliographically approved
Börjesson, A., Erdtman, E., Ahlström, P., Berlin, M., Andersson, T. & Bolton, K. (2013). Molecular modelling of oxygen and water permeation in polyethylene. Polymer, 54(12), 2988
Open this publication in new window or tab >>Molecular modelling of oxygen and water permeation in polyethylene
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2013 (English)In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 54, no 12, p. 2988-Article in journal (Refereed)
Abstract [en]

Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

Place, publisher, year, edition, pages
Elsevier, 2013
Keywords
Permeability, Polyethylene, Molecular simulation, Resursåtervinning, Computational modelling
National Category
Theoretical Chemistry Materials Chemistry Atom and Molecular Physics and Optics
Research subject
Resource Recovery
Identifiers
urn:nbn:se:hb:diva-1569 (URN)10.1016/j.polymer.2013.03.065 (DOI)000319365900020 ()2320/12338 (Local ID)2320/12338 (Archive number)2320/12338 (OAI)
Note

Sponsorship:

KK-stiftelsen

Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2017-12-01
Erdtman, E., Gebäck, T. & Ahlström, P. (2012). Atomistic Modelling of Protein Superabsorbents. In: : . Paper presented at European Symposium on Applied Thermodynamics the ESAT 2012 Potsdam, Tyskland.
Open this publication in new window or tab >>Atomistic Modelling of Protein Superabsorbents
2012 (English)Conference paper, Poster (with or without abstract) (Other academic)
Keywords
Protein, Superabsorbents, Monte Carlo Simulation
National Category
Theoretical Chemistry Other Chemical Engineering
Research subject
Resource Recovery
Identifiers
urn:nbn:se:hb:diva-6876 (URN)2320/11664 (Local ID)2320/11664 (Archive number)2320/11664 (OAI)
Conference
European Symposium on Applied Thermodynamics the ESAT 2012 Potsdam, Tyskland
Available from: 2015-12-22 Created: 2015-12-22 Last updated: 2017-01-22Bibliographically approved
Tian, B.-X., Erdtman, E. & Eriksson, L. A. (2012). Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations. Journal of Physical Chemistry B, 116(40), 12105-12112
Open this publication in new window or tab >>Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations
2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 40, p. 12105-12112Article in journal (Refereed) Published
Abstract [en]

Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

Place, publisher, year, edition, pages
American Chemical Society, 2012
Keywords
Enzymes, QM/MM, Simulation, Reaction mechanism, Porphobilinogen synthase, Resursåtervinning
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:hb:diva-1418 (URN)10.1021/jp304743c (DOI)000309648900005 ()22974111 (PubMedID)2320/11733 (Local ID)2320/11733 (Archive number)2320/11733 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2017-10-17Bibliographically approved
Erdtman, E., Chelakara Satyanarayana, K. & Bolton, K. (2012). Simulation of α- and β-PVDF melting mechanisms. Polymer, 53(14), 2919-2926
Open this publication in new window or tab >>Simulation of α- and β-PVDF melting mechanisms
2012 (English)In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 53, no 14, p. 2919-2926Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics (MD) simulations have been used to study the melting of α- and β-poly (vinylidene fluoride) (α- and β-PVDF). It is seen that melting at the ends of the polymer chains precedes melting of the bulk crystal structure. Melting of α-PVDF initially occurs via transitions between the two gauche dihedral angles (G ↔ G′) followed by transitions between trans and gauche dihedral angles (T ↔ G/G′). Melting of β-PVDF initially occurs via T → G/G′ transitions and via transitions of complete β- (TTTT) to α- (TGTG') quartets. The melting point of β-PVDF is higher than that of α-PVDF, and the simulated melting points of both phases depend on the length of the polymer chains used in the simulations. Since melting starts at the chain ends, it is important to include these in the simulations, and simulations of infinitely long chains yield melting points far larger than the experimental values (at least for periodic cells of the size used in this work), especially for β-PVDF. The simulated heats of fusion are in agreement with available experimental data.

Place, publisher, year, edition, pages
Elsevier Ltd, 2012
Keywords
Poly(vinylidene fluoride), Melting mechanism, Molecular simulation, Resursåtervinning
National Category
Materials Chemistry
Identifiers
urn:nbn:se:hb:diva-1387 (URN)10.1016/j.polymer.2012.04.045 (DOI)000305590000014 ()2320/11643 (Local ID)2320/11643 (Archive number)2320/11643 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2017-12-01
Erdtman, E., Gebäck, T. & Ahlström, P. (2011). Computational modeling of Protein based super-absorbents from waste. Paper presented at Thermodynamics2011, September 1st – September 3rd 2011, Athens, Greece. Paper presented at Thermodynamics2011, September 1st – September 3rd 2011, Athens, Greece.
Open this publication in new window or tab >>Computational modeling of Protein based super-absorbents from waste
2011 (English)Conference paper, Poster (with or without abstract) (Other academic)
Abstract [en]

Hydrogels are used for various applications, for example as transporters in drug delivery, in control lenses, and as superabsorbent material in diapers.[1] Most synthetic produced hydrogels are based on synthetic polymers. Even though they are efficient and cheap, they are not biodegradable and sometimes even toxic. To produce more environmental friendly and biodegradable superabsorbent polymers (Bio- SAPs), other building blocks can be used, such as polysaccharides[2] and various protein structures, for example fish shells[3], collagen[4], soy protein[5] and egg protein[6]. Experimental studies at the University of Boras show that it is possible to produce Bio-SAPs from by-products of ethanol production from ligno-cellulose.[2, 6, 7] 2. Method We have studied the absorption properties of protein structures in silico as a comparison to experimental studies. The NPT Gibbs Ensemble Monte Carlo (GEMC) simulation scheme with two phases is used in order to calculate the absorption capacity of the protein. Pure water was simulated in the first GEMC-phase and the peptide in the second phase. The simulations were made with SPC/E water model [8] and the AMBER99 atomistic force field for the peptides [9]. Furthermore, mesoscopic studies with coarse grained force fields have been done. To facilitate faster computations, we used cell lists for the atom-atom interactions, configurational bias algorithm to build the water molecules and the peptide side-chains, and the cavity bias algorithm [10] for molecule insertions. Model peptides have been studied with varying secondary structure, temperature and protonation (pH). We also plan to study how cross-links affect the absorption. One of the peptides we study is a 20 amino acid long peptide called SSP1.[11] This peptide is designed to form a fibrous structure a hydrogel, and its structure is well defined. We have also studied a peptide which changes secondary structure when changing the pH, and concentration.[12] This makes it possible to compare absorption properties with respect to the secondary structure. 3. Conclusion We have simulated peptides with the Gibbs Ensemble Monte Carlo scheme in order to study the water absorption rate dependent of structure, charge, pH and temperature. This information is useful when developing new biodegradable superabsorbent materials.

Keywords
superabsorbents, gibbs ensemble monte carlo, resouce recovery, Energi och material
National Category
Theoretical Chemistry Other Industrial Biotechnology
Research subject
Resource Recovery
Identifiers
urn:nbn:se:hb:diva-6609 (URN)2320/9127 (Local ID)2320/9127 (Archive number)2320/9127 (OAI)
Conference
Thermodynamics2011, September 1st – September 3rd 2011, Athens, Greece
Available from: 2015-12-22 Created: 2015-12-22
Erdtman, E., Bushnell, E. & Eriksson, L. (2011). Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase. Computational and Theoretical Chemistry, 963(2), 479-489
Open this publication in new window or tab >>Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
2011 (English)In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2, p. 479-489Article in journal (Refereed) Published
Abstract [en]

Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however, is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogen synthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for the formation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to 14.0 kcal mol(-1). We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

Place, publisher, year, edition, pages
Elsevier Science BV, 2011
National Category
Other Basic Medicine
Identifiers
urn:nbn:se:hb:diva-1233 (URN)10.1016/j.comptc.2010.11.015 (DOI)2320/10232 (Local ID)2320/10232 (Archive number)2320/10232 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2018-01-10Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9455-9558

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