| 1. |
- Hyvonen, R., et al.
(författare)
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The likely impact of elevated [CO2], nitrogen deposition, increased temperature and management on carbon sequestration in temperate and boreal forest ecosystems: a literature review
- 2007
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Ingår i: New Phytologist. - Cambridge : Wiley. - 0028-646X .- 1469-8137. ; 173:3, s. 463-480
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Forskningsöversikt (refereegranskat)abstract
- Temperate and boreal forest ecosystems contain a large part of the carbon stored on land, in the form of both biomass and soil organic matter. Increasing atmospheric [CO2], increasing temperature, elevated nitrogen deposition and intensified management will change this C store. Well documented single-factor responses of net primary production are: higher photosynthetic rate (the main [CO2] response); increasing length of growing season (the main temperature response); and higher leaf-area index (the main N deposition and partly [CO2] response). Soil organic matter will increase with increasing litter input, although priming may decrease the soil C stock initially, but litter quality effects should be minimal (response to [CO2], N deposition, and temperature); will decrease because of increasing temperature; and will increase because of retardation of decomposition with N deposition, although the rate of decomposition of high-quality litter can be increased and that of low-quality litter decreased. Single-factor responses can be misleading because of interactions between factors, in particular those between N and other factors, and indirect effects such as increased N availability from temperature-induced decomposition. In the long term the strength of feedbacks, for example the increasing demand for N from increased growth, will dominate over short-term responses to single factors. However, management has considerable potential for controlling the C store.
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| 2. |
- Schyman, Patric, et al.
(författare)
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Hydrogen Abstraction from Deoxyribose by a Neighbouring Uracil-5-yl Radical
- 2007
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 9, s. 5975-5979
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen abstraction from the C1 and C2 positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5-AU-3 DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1 and C2. When adenine is neutral there is a preference for the C1 site and when the adenine is a radical cation the C2 site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1 is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1 the preferred site for abstraction.
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| 3. |
- Lyubartsev, Alexander, 1962-, et al.
(författare)
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Hierarchical multiscale modelling scheme from first principles to mesoscale
- 2009
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Ingår i: Journal of Computational and Theoretical Nanoscience. - : American Scientific Publishers. - 1546-1955 .- 1546-1963. ; 6:5, s. 951-959
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Tidskriftsartikel (refereegranskat)abstract
- We present a straight-forward implementation of a practical hierarchical multiscale modelling scheme which enables us to start from first-principles atomistic computer simulation and successively coarse-grain the model by leaving out uninteresting degrees of freedom. Using the Car-Parrinello method or our recently developed highly efficient tight-binding-like approximate density-functional quantum mechanical method,w e first perform first-principles simulations we obtain a set of atomistic pair-wise effective interaction potentials to be used as a force field with scaling up the system size 2–3 orders of magnitude. The atomistic simulations similarly provide a new set of effective potentials but at a chosen coarse-grain level suitable for large-scale mesoscopic or soft-matter simulations beyond the atomic resolution. Show several examples are shown of how this scheme is done based on effective interaction potentials to tie together the various scales of modelling.
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| 4. |
- Albet-Torres, Nuria, et al.
(författare)
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Molecular motors on lipid bilayers and silicon dioxide: different driving forces for adsorption
- 2010
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 6:14, s. 3211-3219
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how different types of interactions govern adsorption of the myosin motor fragment heavy meromyosin (HMM) onto different substrates is important in functional studies of actomyosin and for the development of motor powered lab-on-a-chip applications. In this study, we have combined in vitro motility assays and quartz crystal microbalance with dissipation (QCM-D) monitoring to investigate the underlying adsorption mechanisms of HMM onto supported lipid bilayers in comparison with pure and silanized SiO2. The QCM-D results, combined with data showing actin transportation by HMM adsorbed onto positively charged supported lipid bilayers, suggest reversible HMM surface adsorption via the negatively charged coiled-coil tail region. In contrast, the QCM-D data for HMM adsorption onto negatively charged lipids support a model according to which HMM adsorbs onto negatively charged surfaces largely via the positively charged actin binding regions. Adsorption studies at low (30-65 mM) and high (185-245 mM) ionic strengths onto piranha cleaned SiO2 surfaces (contact angle
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| 5. |
- Erdtman, Edvin, et al.
(författare)
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Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase
- 2011
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Ingår i: Computational and Theoretical Chemistry. - Amsterdam : Elsevier. - 2210-271X .- 2210-2728. ; 963:2-3, s. 479-489
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Tidskriftsartikel (refereegranskat)abstract
- 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 porphobilinogensynthase (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 theformation 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 to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.
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| 6. |
- Eriksson, Leif A., 1964-, et al.
(författare)
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Tetrazole derivatives as cytochrome p450 inhibitors
- 2019
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Patent (populärvet., debatt m.m.)abstract
- According to the invention there is provided a compound of formula I, wherein R1 and R2 have meanings given in the description, which compounds are useful in the treatment of skin disorders and other diseases.
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| 7. |
- Aissaoui, Nesrine, 1983, et al.
(författare)
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FRET enhancement close to gold nanoparticles positioned in DNA origami constructs
- 2017
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Ingår i: Nanoscale. - Cambridge, United Kingdom : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 9:2, s. 673-683
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Tidskriftsartikel (refereegranskat)abstract
- Here we investigate the energy transfer rates of a Förster resonance energy transfer (FRET) pair positioned in close proximity to a 5 nm gold nanoparticle (AuNP) on a DNA origami construct. We study the distance dependence of the FRET rate by varying the location of the donor molecule, D, relative to the AuNP while maintaining a fixed location of the acceptor molecule, A. The presence of the AuNP induces an alteration in the spontaneous emission of the donor (including radiative and non-radiative rates) which is strongly dependent on the distance between the donor and AuNP surface. Simultaneously, the energy transfer rates are enhanced at shorter D-A (and D-AuNP) distances. Overall, in addition to the direct influence of the acceptor and AuNP on the donor decay there is also a significant increase in decay rate not explained by the sum of the two interactions. This leads to enhanced energy transfer between donor and acceptor in the presence of a 5 nm AuNP. We also demonstrate that the transfer rate in the three "particle" geometry (D + A + AuNP) depends approximately linearly on the transfer rate in the donor-AuNP system, suggesting the possibility to control FRET process with electric field induced by 5 nm AuNPs close to the donor fluorophore. It is concluded that DNA origami is a very versatile platform for studying interactions between molecules and plasmonic nanoparticles in general and FRET enhancement in particular.
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| 8. |
- Birgersson, Evert, et al.
(författare)
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Binary fission-fragment yields from the reaction 251Cf(nth, f)
- 2005
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Ingår i: Nuclear fission and fission-product spectroscopy. - : American Institute of Physics. - 0735402884 ; , s. 349-352
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Konferensbidrag (refereegranskat)abstract
- The recoil mass spectrometer LOHENGRIN of the Laue-Langevin Institute, Grenoble has been used to measure the light fission-fragment mass yield and kinetic energy distributions from neutron-induced 252Cf*, using 251Cf as target material. ©2005 American Institute of Physics
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| 9. |
- Birgersson, Evert, et al.
(författare)
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Light fission-fragment mass distribution from the reaction 251Cf(nth, f)
- 2007
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Ingår i: Nuclear Physics A. - Amsterdam : Elsevier. - 0375-9474 .- 1873-1554. ; 791:1-2, s. 1-23
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Tidskriftsartikel (refereegranskat)abstract
- For mass numbers A = 80 to 124 the recoil mass spectrometer LOHENGRIN of the Institute Laue-Langevin in Grenoble was used to measure with high resolution the light fission-fragment mass yields and kinetic energy distributions from thermal-neutron induced fission of 252Cf* for the first time, using 251Cf as target material. The obtained mean light fragment mass AL = (107 ± 2) and the corresponding mean kinetic energy Ek,L = (103±2) MeV are within the expected trend. Emission yields around A = 115 are enhanced and the corresponding mean kinetic energy is higher compared to spontaneous fission of 252Cf. This could be explained by the existence of an additional super-deformed fission mode.
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| 10. |
- Li, Xin, et al.
(författare)
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Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2 : A Theoretical Study
- 2009
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Ingår i: Journal of Physical Chemistry B. - Washington, D. C. : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:31, s. 10916-10922
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Tidskriftsartikel (refereegranskat)abstract
- We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.
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