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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 5840-5850 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 664-666 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: tRNASec is a UGA suppressor tRNA which co-translationally inserts selenocysteine into proteins. Its eight-base-pair tRNASec acceptor stem, which contains key recognition elements, was synthesized using solid-phase phosphoramidite RNA chemistry. High-resolution X-ray diffraction data were collected using synchrotron radiation under cryogenic cooling conditions. The crystals diffract to a maximal resolution of 1.8 Å. X-ray diffraction data were processed to 2.4 Å. tRNASec microhelix crystallizes in space group R32, with cell constants a = 47.02, b = 47.02, c = 373.03 Å, α = β = 90, γ = 120°. The crystals contain three RNA molecules per asymmetric unit.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1405-1413 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An RNA helix with seven base pairs which was derived from the acceptor stem of Escherichia coli tRNAAla, rGGGGCUA·rUAGCUCC (ALAwt), as well as a variant, rGGGGCUA·rUAGCCCC (ALAC70), in which the single G·U wobble base pair of ALAwt was replaced by G·C, crystallize in space group C2. Both non-isomorphic crystal forms display a complex packing pattern, which can be described alternatively as disorder or pseudo-merohedral twinning. The structure of ALAwt was determined by SIRAS phasing using an isomorphous iodine derivative, rGGGGCi5UA·rUAGCUCC (ALAI). All three RNA structures were subsequently subjected to twin refinement in space group P1, using anisotropic thermal displacement parameters at resolutions of 1.16, 1.23 and 1.4 Å for ALAwt, ALAI and ALAC70, respectively. Alternatively, the structure of ALAwt was refined in space group C2 assuming twofold disorder of the molecular orientation. The refined structures are of reasonable quality according to all available indicators. There are no systematic differences between the molecular models resulting from twin refinement and disorder refinement.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 77-88 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The unphysical flow of zero-point energy (ZPE) in classical trajectory calculations is a consequence of the fact that the classical phase-space distribution may enter regions of phase space that correspond to a violation of the uncertainty principle. To restrict the classically accessible phase space, we employ a reduced ZPE γεZP, whereby the quantum correction γ accounts for the fraction of ZPE included. This ansatz is based on the theoretical framework given in Paper I [G. Stock and U. Müller, J. Chem. Phys. 111, 65 (1999), preceding paper], which provides a general connection between the level density of a system and its relaxation behavior. In particular, the theory establishes various criteria which allows us to explicitly calculate the quantum correction γ. By construction, this strategy assures that the classical calculation attains the correct long-time values and, as a special case thereof, that the ZPE is treated properly. As a stringent test of this concept, a recently introduced classical description of nonadiabatic quantum dynamics is adopted [G. Stock and M. Thoss, Phys. Rev. Lett. 78, 578 (1997)], which facilitates a classical treatment of discrete quantum degrees of freedom through a mapping of discrete onto continuous variables. Resulting in negative population probabilities, the quasiclassical implementation of this theory significantly suffers from spurious flow of ZPE. Employing various molecular model systems including multimode models with conically intersecting potential-energy surfaces as well as several spin-boson-type models with an Ohmic bath, detailed numerical studies are presented. In particular, it is shown, that the ZPE problem indeed vanishes, if the quantum correction γ is chosen according to the criteria established in Paper I. Moreover, the complete time evolution of the classical simulations is found to be in good agreement with exact quantum-mechanical calculations. Based on these studies, the general applicability of the method, the performance of the classical description of nonadiabatic quantum dynamics, as well as various issues concerning classical and quantum ergodicity are discussed. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 6230-6245 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A mixed quantum-classical description of nonadiabatic photoreactions such as internal conversion and electron transfer is outlined. In particular the validity and limitations of Tully's surface-hopping (SH) model [J. Chem. Phys. 93, 1061 (1990)] is investigated in the case of photoinduced relaxation processes which are triggered by a multidimensional conical intersection (or avoided crossing) of two potential-energy surfaces. Detailed numerical studies are presented, adopting (i) a three-mode model of the S2→S1 internal-conversion process in pyrazine, (ii) a multimode model of ultrafast intramolecular electron-transfer, (iii) a model exhibiting nonadiabatic photoisomerization dynamics, and (iv) various spin-boson-type models with an Ohmic bath for the description of electron-transfer in solution. The SH simulations are compared to exact quantum-mechanical calculations as well as to results obtained by an alternative mixed quantum-classical description, that is, the self-consistent classical-path method. In all cases, the SH data are shown to reproduce the quantum results at least qualitatively; in some cases the SH results are in quantitative agreement with the complex electronic and vibrational relaxation dynamics exhibited by the quantum calculations. Depending on the physical situation under consideration, either the SH or the self-consistent classical-path method was found to be superior. The characteristic features of a mixed quantum-classical description of photoinduced bound-state dynamics (e.g., the start of the trajectories on a diabatic electronic potential-energy surface, high chance of a trajectory undergoing multiple electronic transitions) as well as the specific problems of the SH approach are discussed in some detail. In particular, the focus is on the ability of a method to account for the branching of trajectories, to correctly describe the electronic phase coherence and the vibrational motion on coupled potential-energy surfaces, and to obey the principle of microreversibility. Furthermore, an alternative way to handle classically forbidden electronic transitions is proposed, which is shown to lead to significantly better results than the usual procedure. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 7516-7526 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A mixed quantum-classical formulation of nonadiabatic molecular processes is outlined. Based on a recently introduced mapping formalism [Stock and Thoss, Phys. Rev. Lett. 78, 578 (1997)], the formulation employs a quantum-mechanically exact mapping of discrete electronic states onto continuous variables, thus describing the dynamics of both electronic and nuclear degrees of freedom by continuous variables. It is shown that the classical evaluation of the mapping formalism results in a self-consistent description of electronic and nuclear degrees of freedom, which treats both types of dynamical variables in a completely equivalent way. The applicability of the approach is thus solely determined by the validity of the classical approximation and does not rest on additional assumptions such as the ad hoc combination of classical and quantum-mechanical theories. The observation of unrestricted flow of zero-point energy in the electronic degrees of freedom indicates the limits of the classical approximation. However, it is shown that this problem can virtually be removed by restricting the classically accessible phase-space. Adopting a multidimensional model of the internal-conversion process in the benzene cation, it is demonstrated that the classical mapping approach is able to account for the branching of classical trajectories in the presence of multiple surface crossings. The classical simulations are found to match the exact quantum-mechanical reference calculations quite accurately. The virtues and limitations of various mixed quantum-classical descriptions are discussed by comparing the mapping approach to the classical-path, the classical electron-analog, and the surface-hopping formulation, respectively. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 65-76 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Necessary conditions under which a classical description will give the correct quantum relaxation behavior are analyzed. Assuming a nonequilibrium preparation, it is shown that the long-time mean values of observables can be expressed in terms of the spectral density and state-specific level densities of the system. Any approximation that reproduces these quantities therefore yields the correct expectation values at long times. Apart from this rigorous condition, a weaker but more practical criterion is established, that is, to require that the total level density is well approximated in the energy range defined by the spectral density. Since the integral level density is directly proportional to the phase-space volume that is energetically accessible to the system, the latter condition means that an appropriate classical approximation should explore the same phase-space volume as the quantum description. In general, however, this is not the case. A well-known example is the unrestricted flow of zero-point energy in classical mechanics. To correct for this flaw of classical mechanics, quantum corrections are derived which result in a restriction of the classically accessible phase space. At the simplest level of the theory, these corrections are shown to correspond to the inclusion of only a fraction of the full zero-point energy into the classical calculation. Based on these considerations, a general strategy for the classical simulation of quantum relaxation dynamics is suggested. The method is (i) dynamically consistent in that it refers to the behavior of the ensemble rather than to the behavior of individual trajectories, (ii) systematic in that it provides (rigorous as well as minimal) criteria which can be checked in a practical calculation, and (iii) practical in that it retains the conceptional and computational simplicity of a standard quasiclassical calculation. Employing various model problems which allow for an analytical evaluation of the quantities of interest, the virtues and limitations of the approach are discussed. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 298 (1982), S. 582-585 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The sequenced genomes of bacteriophages OX174 (ref. 12), G4 (ref. 13) and fd (ref. 14) and of the eukaryotic viruses simian virus 40 (SV40)15 and polyoma16 were searched by computer for invert repeat DNA sequences, which can form hairpin (or cruciform)2-like secondary structures. The search was ...
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature America Inc.
    Nature structural biology 7 (2000), S. 380-383 
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Thermophilic organisms produce proteins of exceptional stability. To understand protein thermostability at the molecular level we studied a pair of cold shock proteins, one of mesophilic and one of thermophilic origin, by systematic mutagenesis. Although the two proteins differ in sequence at ...
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1546-1696
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: [Auszug] Nucleic acid diagnostics is dominated by fluorescence-based assays that use complex and expensive enzyme-based target or signal-amplification procedures. Many clinical diagnostic applications will require simpler, inexpensive assays that can be done in a screening mode. We have developed a ...
    Type of Medium: Electronic Resource
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