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  • 1
    Electronic Resource
    Electronic Resource
    On the uniqueness of the Reverse Monte Carlo simulation. I. Simple liquids, partial radial distribution functions (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 3042-3049 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Partial radial distribution functions of standard Monte Carlo simulations were used as input for Reverse Monte Carlo simulation, a novel method for structural modeling. From detailed comparison of the two independent (MC and RMC) particle configurations it has turned out that sufficiently close agreement in radial distribution functions involves deeper structural similarities. RMC results, i.e., particle configurations produced by RMC upon the basis of partial radial distribution functions, are therefore applicable for detailed analysis of the structure, giving new prospects for data evaluation in neutron diffraction method. As a result of extensive Reverse Monte Carlo simulations of this work some new aspects of the technique itself could be revealed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.459827
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular dynamics analog of the reverse Monte Carlo method (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 2027-2035 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new molecular dynamics algorithm is reported to evaluate data of diffraction experiments on liquids or amorphous materials. The atoms, in addition to the excluding short-range forces, are moved in a fictitious potential field defined by the chi-square difference of the experimental structure factors. The results provided by the new reverse molecular dynamics algorithm are equivalent to those obtained using the reverse Monte Carlo method for the test model systems of the Lennard-Jones liquid and water. We exploited the test calculations of the water system to discuss the separation capabilities of these modeling techniques. The results were encouraging, if the number of different (good quality) experimental functions as input information is larger or equivalent with the number of particle pair-correlation functions necessary to characterize the structure of the system. However, the results indicated dubious outcomes, if there were more partials estimated than different experimental data sets. This questions the conclusions of some previous studies. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1337044
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  • 3
    Electronic Resource
    Electronic Resource
    Determination of pair-potential parameters from experimental structure factors (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 4770-4775 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method is developed to obtain pair-potential parameters for liquids from structure factors measured by diffraction experiments. The approach is a generalization of the method of Lyubartsev and Laaksonen [Phys. Rev. E 52, 3730 (1995)]. Each step of the iterative process consists of two parts: a Monte Carlo or molecular dynamics simulation with an assumed pair-potential and the modification of the potential due the experimental data and different quantities calculated in the simulations. The choice of the structure factor as input function makes it possible to avoid the difficulties of the Fourier transformation from the inverse to the real space, to replace the solution of the set of linear equations with simple linear combination in the case of multicomponent or molecular systems, and to use least-square fit for the modification of the pair-potential. The latter is less sensitive to the errors of the data than the unique solution of linear equations applied in the original recipe. The method is tested for one- and two-component Lennard-Jones systems, and Lennard-Jones parameters for liquid argon are determined from a diffraction experiment. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1391453
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  • 4
    Electronic Resource
    Electronic Resource
    Comment on "A new algorithm for reverse Monte Carlo simulations" [J. Chem. Phys. 109, 2624 (1998)] (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 5620-5621 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The purpose of the reverse Monte Carlo method is to help in processing experimental data obtained from x-ray or neutron diffraction measurements and setup three-dimensional models plausible with chemical evidence and the results of the measurement. Although the "inverse theorem" provides certain theoretical footage to the method, it says nothing about the correct numerical details of the RMC algorithm. Unfortunately, the latter quality opens up opportunity for methodological studies with results of questionable values. Thus, we felt obliged to point to the problematic features of the paper of da Silva et al. [J. Chem. Phys. 109, 2624 (1998)] with the aim to draw the attention of the entire scientific community dealing with structural modeling. The debate can be very useful in clarifying the problematic details of the frequently criticized reverse Monte Carlo technique. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.479826
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  • 5
    Electronic Resource
    Electronic Resource
    Determination of the radial distribution function of small-particle polymer latices using reverse Monte Carlo simulation (1992)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 96 (1992), S. 7150-7153 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100197a002
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  • 6
    Electronic Resource
    Electronic Resource
    Novel semiempirical method for quantum Monte Carlo simulation: Application to amorphous silicon (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 3742-3746 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We propose a novel bulk phase Monte Carlo simulation technique, in which the energy is calculated by quantum mechanical methods. The semiempirical fragment self-consistent field technique applied divides the periodic simulation cell into two parts. The first is the subsystem where the important change (the random movement of an atom or molecule) takes place and the second is the environment exerting only secondary effects on the former. Expanding the electronic wave function on the basis of strictly localized molecular orbitals and/or atomic hybrid orbitals the wave function of the environment is obtained from simple coupled 2×2 secular equations. The conventional self-consistent field equations, with a perturbation term in the Fockian, have to be solved only for the subsystem. In this way the computational efforts are decreased drastically, as the dependence on the number of atoms in the environment reduces to quadratic instead of cubic or quartic as in conventional semiempirical or ab initio methods, respectively. We wrote a computer code and applied our method to amorphous silicon. Starting from a distorted tetrahedrally bonded random network model we performed Monte Carlo simulations using the fragment self-consistent field energy calculation. After equilibration we obtained distribution functions almost identical to the ones corresponding to the distortion free tetrahedrally bonded network. This finding confirms the adequacy of our method for this specific case.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466361
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  • 7
    Electronic Resource
    Electronic Resource
    Fluctuation of the pair-correlation function (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 8575-8576 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using a simple thermodynamic argument we derive an expression providing the r-dependent fluctuations of the pair-correlation function, g(r), of a liquid. The variance of g(r) at r is a function only of its own value at this point. Fluctuations calculated from Monte Carlo simulations fit well to this formula. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.475009
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  • 8
    Electronic Resource
    Electronic Resource
    Ab initio pair potential parameter set for the interaction of a rigid and a flexible water model and the complete series of the halides and alkali cations (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 5518-5524 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ab initio calculations were performed at the quantum chemical levels of the second and fourth order Moller–Plesset perturbation theory. The binding energies were corrected for the basis set superposition error. Exactly 420 different ion–water configurations were chosen for each ion to scan the potential surface entirely. The parametrized analytical potential functions, the radial distribution functions, and the solvation internal energies obtained by molecular dynamics simulations were compared to previous simulations and experimental results. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472392
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  • 9
    Electronic Resource
    Electronic Resource
    Conceptual and technical improvement of the reverse Monte Carlo algorithm (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 7402-7408 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We performed Metropolis Monte Carlo and a comprehensive set of reverse Monte Carlo simulations using the same Lennard-Jones liquid to analyze the algorithmic correctness of the latter method. We found that the present reverse Monte Carlo technique is biased because it samples relatively disordered arrangements more often than ordered ones, which leads to a poor acceptance ratio and questionable relevance to the structure of the real system. On the basis of our results, we propose changes in the algorithm. To remove the deficiency we applied a combined acceptance criterion, which in addition to the very restrictive difference minimization procedure, uses an entropy related factor to select from the possible configurations. Further improvement can be achieved if the simulations are performed on the structure factor and the radial distribution function simultaneously. If the radial distribution function is the target function, incorporation of the r-dependent measurement error in the acceptance criterion is essential to obtain results similar in quality to the structure function techniques. The modifications enhance the performance of the reverse Monte Carlo method without increasing the computational effort. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474978
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  • 10
    Electronic Resource
    Electronic Resource
    Difficulties in coupling to conformationally constrained aromatic amino acids (2000)
    Springer
    International journal of peptide research and therapeutics 7 (2000), S. 157-163 
    Details
    ISSN: 1573-3904
    Keywords: difficult coupling ; ‘difficult sequence’ ; elevated temperature ; HATU ; HOAt ; HOTic ; Tic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Coupling of amino acids to 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic) and 1,2,3,4-tetrahydro-7-hydroxyisoquinoline-3-carboxylic acid (HOTic) is difficult. In model experiments, use of 1-hydroxy-7-azabenzotriazole (HOAt) in combination with eitherN,N-diisopropylcarbodiimide (DIC) orO-(7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyluronium (HATU) for activation was effective in solving coupling difficulties. Based on this finding, HOTic was then incorporated into the 20–31 fragment of human epidermal growth factor (hEGF). [Abu20, 31,HOTic22]hEGF(20–31)-NH2 was shown to be a ‘difficult sequence’, but replacement of the Tyr at position 29 with HOTic facilitates the complete dodecapeptide synthesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443583
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