| 1. |
- Björk, Glenn R, et al.
(författare)
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A primordial tRNA modification required for the evolution of life?
- 2001
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Ingår i: EMBO Journal. - : Wiley. - 0261-4189 .- 1460-2075. ; 20:1-2, s. 231-239
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of reading frame maintenance must have been an early event, and presumably preceded the emergence of the three domains Archaea, Bacteria and Eukarya. Features evolved early in reading frame maintenance may still exist in present-day organisms. We show that one such feature may be the modified nucleoside 1-methylguanosine (m(1)G37), which prevents frameshifting and is present adjacent to and 3' of the anticodon (position 37) in the same subset of tRNAs from all organisms, including that with the smallest sequenced genome (Mycoplasma genitalium), and organelles. We have identified the genes encoding the enzyme tRNA(m(1)G37)methyltransferase from all three domains. We also show that they are orthologues, and suggest that they originated from a primordial gene. Lack of m(1)G37 severely impairs the growth of a bacterium and a eukaryote to a similar degree. Yeast tRNA(m(1)G37)methyltransferase also synthesizes 1-methylinosine and participates in the formation of the Y-base (yW). Our results suggest that m(1)G37 existed in tRNA before the divergence of the three domains, and that a tRNA(m(1)G37)methyltrans ferase is part of the minimal set of gene products required for life.
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| 2. |
- Håkansson, P, et al.
(författare)
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Itô diffusions on hypersurfaces with application to the Schwarz-P surface and nuclear magnetic resonance theory
- 2002
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Ingår i: The Journal of Chemical Physics. ; 117:19, s. 8634-43
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Tidskriftsartikel (refereegranskat)abstract
- This work presents a new Brownian dynamics simulation method of translational diffusion on curved surfaces. This new method introduce any implicit defined surface into the stochastic differential equation describing Brownian motion on that surface. The surface curvature will thus enter the force term (A) in the stochastic differential equation dXt = A(Xt)dt + B(Xt)dWt describing an Itô process. We apply the method calculating time correlation functions relevant in nuclear magnetic resonance (NMR) relaxation and translational diffusion studies of cubic phases of lyotropic systems. In particularly we study some bicontinuous cubic liquid crystalline phases which can be described as triply periodic minimal surfaces. The curvature dependent spin relaxation of the Schwarz-P minimal surface is calculated. A comparison of relaxation is made with the more complex topology of the Neovius surface which is another minimal surface in the same space group, and with parallel displacement of the minimal surface which thus results in a nonminimal surface. The curvature dependent relaxation effects are determined by calculating the translational diffusion modulated time-correlation function which determine the relaxation rates of a quadrupole nuclei residing in the water–lipid interface. The results demonstrates that spin relaxation data can provide quantitative information about micro-structure of biocontinuous cubic phases and that it is sensitive to the topology of the surface and to parallel displacement of the model surface. Consequently, spin relaxation may be used as a complement to x-ray diffraction in order to discriminate between different microstructures. It is concluded that fast and accurate computer simulations experiments is needed to be able to interpret NMR relaxation experiments on curved surfaces. © 2002 American Institute of Physics.
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| 3. |
- Persson, P. O., et al.
(författare)
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Simulation of a waveguide filter using wavelet-based numerical homogenization
- 2001
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 166:2, s. 361-382
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Tidskriftsartikel (refereegranskat)abstract
- We apply wavelet-based numerical homogenization to the simulation of an optical waveguide filter. We use the method to derive approximate one-dimensional models and subgrid models of the filter. Numerical examples of the technique are presented, and the computational gains are investigated.
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