| 1. |
- Thaning, Johan, et al.
(författare)
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Molecular Conformations in a Phospholipid Bilayer Extracted from Dipolar Couplings: A Computer Simulation Study
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society. - 1520-6106 .- 1520-5207. ; 111:48, s. 13638-13644
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom−atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the “true” distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.
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| 2. |
- Asplund, Maria, 1978-, et al.
(författare)
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Biocompatibility of PEDOT/biomolecular composites intended for neural communication electrodes
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Annan publikation (populärvet., debatt m.m.)abstract
- Electrodes of the conjugated polymer poly(3,4-ethylene dioxythiophene) (PEDOT) have been shown to possess very attractive electrochemical properties for functional electrical stimulation (FES) or recording in the nervous system. Biomolecules already present in nervous tissue, added as counter ions in PEDOT electropolymerisation, could be a route to further improve the biomaterial properties of PEDOT, eliminating the need of surfactant counter ions like docedyl benzene sulphonate (DBS) or polystyrene sulphonate (PSS) in the polymerisation process. Such PEDOT/biomolecular composites using heparin, or hyaluronic acid, have been electrochemically investigated in a previous study and have been shown to retain the attractive electrochemical properties already proven for PEDOT:PSS. The aim of the present study is to evaluate biocompatibility of these PEDOT/biomolecular composites in vitro and also evaluate PEDOT:heparin biocompatibility in cortical tissue in vivo. Hereby, we also aim to identify a suitable test protocol, that can be used in future evaluations when further material developments are made. Material toxicity was first tested on cell lines, both through a standardised agarose overlay assay on L929 fibroblasts, and through elution tests on human neuroblastoma SH-SY5Y cells. Subsequently, a biocompatibility in vivo test was performed using PEDOT:heparin coated platinum probes implanted in the cerebral cortex of Sprague-Dawley rats. Tissue was collected at three weeks and six weeks of implantation and evaluated by immunohistochemistry. No cytotoxic response was seen to any of the PEDOT:biomolecular composites tested here. Furthermore, elution tests were found to be a practical and effective way of screening materials for toxicity and had a clear advantage over the agarose overlay assay, which was difficult to apply on other cell types than fibroblasts. Elution tests would therefore be recommendable as a screening method, at all stages of material development. In the in vivo tests, the stiffness of the platinum substrate was a significant problem, and extensive glial scarring was seen in most cases irrespective of implant material. However, quantification of immunological response through distance measurements from implant site to closest neuron, and counting of macrophage densities in proximity to polymer surface, was comparable to those of platinum controls. These results indicate that PEDOT:heparin surfaces were as compatible with cortical tissue as pure platinum controls.
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| 3. |
- Dvinskikh, Sergey V., et al.
(författare)
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Mesomorphism in columnar phases studied by solid-state nuclear magnetic resonance
- 2006
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Ingår i: Physical Review E. - : American Physical Society. - 1539-3755. ; 74:2, s. 021703-
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present C-13 and H-1 NMR investigations of 2, 3, 6, 7, 10, 11-hexahexyl-thiotriphenylene (HHTT). The measurements were carried out under both static and magic-angle spinning conditions. The phase diagram of HHTT is K <-> H <-> D-hd <-> I, where H is a helical phase and D-hd is a columnar liquid crystal. The motivation was to characterize the molecular order and dynamics and to investigate differences at the molecular level between the two mesophases: H and D-hd. It is shown that D-hd is a conventional columnar liquid crystal, where the molecular core undergoes fast rotation about the symmetry axis. The orientational order in this mesophase is lower and the temperature dependence of the order parameter is steeper than in other triphenylene-based compounds. On the other hand, in the helical phase the core, similarly to the solid phase, is essentially rigid. The difference between the solid and helical phases is mainly manifested in an increased mobility of the aliphatic chains observed in the latter phase. In addition, the sample exhibits thermal history effects, which are observed in the different behavior upon cooling and heating.
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| 4. |
- Thaning, Johan, et al.
(författare)
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Molecular structure extracted from residual dipolar couplings: Diphenylmethane dissolved in a nematic liquid crystal
- 2005
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics. - 0021-9606 .- 1089-7690. ; 123:4, s. 044507-
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes an analysis of 1H–1H residual dipolar couplings (RDCs)in diphenylmethane (DPM) dissolved in a nematic liquid crystal, reportedby Celebre et al. [J. Chem. Phys. 118, 6417 (2003)]. Inthat article, the conformational distribution function for DPM was extractedfrom the RDCs, using the additive potential (AP) model whichis based on the molecular-field theory. The AP approach isa powerful, and frequently used, tool for analysis of thenuclear-magnetic-resonance (NMR) parameters in liquid crystals. It requires, however, apriori knowledge of the functional form of the torsional potential,which may even for a simple molecule, such as DPM,be complicated to determine. Here, we analyze the same setof the RDCs using our APME procedure, which is ahybrid model based on the AP approach and maximum entropy(ME) theory. The APME procedure does not require any assumptionsabout the functional form of the torsional potential and, incontrast with the ME method, is applicable to weakly orderedsystems. In the investigation reported in the present study, theresults from the APME analysis are in good agreement withthe AP interpretation, whereas the ME approach essentially fails inthe extraction of the conformational distribution function for DPM.
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| 5. |
- Thaning, Johan, 1980-
(författare)
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Molecular Structure in Liquid Crystals Studied by NMR
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is focused on structure determinations of molecules in liquid crystals using NMR. The systems described here exhibit orders ranging from nearly isotropic to essentially solid. The structure is determined by interpreting, mainly dipolar couplings, but also J-couplings and NOE data using conformational distribution functions (cdfs) to capture both the structure and the flexibility of the molecules. The models used in the analysis of the NMR parameters are: a statistical approach denoted Maximum Entropy (ME), a mean field method named Additive Potential (AP) and a synthesis of the two named APME. The thesis covers some background on liquid crystals, NMR, dipolar couplings and their role in structure determination as well as the aforementioned models used for this purpose.The thesis also discusses four papers: 1st being a comparison of the ME, AP and APME models in the structure determination of diphenylmethane. The 2nd covering a test of the APME method, reproducing the cdf of dimyristoylphosphatidylcholine in a lipid bilayer obtained through a molecular dynamics simulation using the APME method on dipolar couplings calculated from the MD trajectory. The 3rd paper deals with a discotic molecule 2, 3, 6, 7, 10, 11-hexahexyl-thiotriphenylene, HHTT displaying a polymorphism which is investigated, using NMR, determining the characteristics of three of its phases. Finally the 4th paper is a structure investigation of α-cyclodextrin employing the ME method using experimental J-couplings, NOEs and dipolar couplings.
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| 6. |
- Thaning, Johan, et al.
(författare)
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NMR Studies of Molecular Conformations in α-Cyclodextrin
- 2008
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society. - 1520-6106 .- 1520-5207. ; 112:29, s. 8434-8436
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Tidskriftsartikel (refereegranskat)abstract
- A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to α-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.
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