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  • 2005-2009  (94)
  • 1995-1999  (146)
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  • 1
    Electronic Resource
    Electronic Resource
    Statistical mechanics on the space of kinetic folding pathways (1995)
    Springer
    Il nuovo cimento della Società Italiana di Fisica 17 (1995), S. 983-991 
    Details
    ISSN: 0392-6737
    Keywords: General, theoretical, and mathematical biophysics (including logic of biosystems, quantum biology, and relevant aspects of thermodynamics, information theory, cybernetics, and bionics) ; Molecular dynamics, conformational changes, and pattern recognition in biomolecules ; Physical chemistry of solutions of biological macromolecules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Summary We introduce a general scheme to assign statistical weights to alla priori pathways in conformation space for an aggregate of interacting particles that undergoes a series of unimolecular events in a limited time frame. Illustrations of such systems are biopolymers that fold intramolecularly or macromolecules of biological relevance that exert their function onto themselves through a series of structural rearrangements under the severe time constraints imposed by enzymatic timing. We endow the space of kinetically controlled pathways with a regular measure induced by a stochastic process built upon a complex potential energy landscape. This process simulates the progressive and opportunistic exploration of basins of attraction of critical points in the molecular potential energy. The derivation is general and holds for any diffusion-like process subject to time constraints and governed by thermal fluctuations upon a complex energy landscape. Within this framework, the ensemble of physically relevant kinetically arrested states becomes a cross-section of the ensemble of pathways at a fixed instant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02456786
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  • 2
    Electronic Resource
    Electronic Resource
    A lumped model for H2/O2 oxidation in the oscillatory regime (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 7006-7016 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A lumped model for H2/O2 oxidation in the oscillatory regime is constructed by using the approach of approximate constrained nonlinear lumping based on an algebraic method within nonlinear perturbation theory. The fast variables approach zero rapidly such that the lumped model is constructed within a slow manifold by setting the identified fast variables to zero. The model dimension is reduced from 7 to 4. The variables representing the concentrations of H2, O2, H2O, and H are explicitly kept unlumped. The lumped model accurately reproduces the main features of the original system, such as oscillatory periods and concentration profiles. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469094
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  • 3
    Electronic Resource
    Electronic Resource
    δ -target optimal control of molecular dynamics: Application to a rotating diatomic molecule (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 8412-8423 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The δ-target method proposed recently [Chem. Phys. Lett. 235, 309 (1995)] was shown to significantly simplify the task of optimal control of molecular localization. The present paper is intended to study the application of the δ-target technique to a practically interesting case of a diatomic molecule including rotation. Illustrative numerical examples are presented for the molecules NO and Na2. The δ-target method is shown to provide good control when the rotational temperature is not too high. The optimal control solution is very robust and insensitive to small changes in the potential curves and transition dipole moment functions. It is shown that the field obtained within the linearized δ-target optimal control technique can be successfully used in the nonlinear regime. The possibility of extending the δ-target technique is considered for treating strong field nonlinear optimal control tasks. The computational advantages of the method are discussed. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470152
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  • 4
    Electronic Resource
    Electronic Resource
    Determining regular orbits in the presence of irregular trajectories using optimal control theory (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 6637-6644 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two general algorithms are presented to determine regular orbits in the presence of irregular trajectories in a phase space of n degrees of freedom. The first algorithm searches for regular orbits with the energy as a free-floating parameter. The second algorithm seeks regular orbits at constant energy. These two approaches utilize optimal control theory to employ a small external control field that permits a search among the irregular motion for the regular orbits. The optimizing algorithm naturally seeks regular orbits with the control field turned off. Numerical results with a chaotic Hamiltonian show the method to be effective in determining regular trajectories. If the system is completely chaotic in some region, the method determines which initial condition is the best one in order to achieve a nearly regular orbit. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470393
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  • 5
    Electronic Resource
    Electronic Resource
    Determination of multiple diabatic potentials by the inversion of atom–atom scattering data (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4052-4060 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An inversion algorithm based on first-order functional sensitivity analysis and Tikhonov regularization is extended for the determination of multiple (diabatic) potentials from elastic and/or inelastic scattering data. Two methods of inversion are presented. In order to illustrate the methods, two-state and three-state models of the He++Ne system are employed in a simulated inversion, the former for the recovery of an entire potential matrix, and the latter to obtain multiple coupling elements, as well as to compare and contrast the two methods against each other. In the case of the two-state model, good agreement between the recovered and the model potentials is achieved if initial guesses for V11(r) and [V22(r)−V22(∞)] are within ±5% of the model, and those for the coupling element V12(r) are within ±10%, thus indicating that the method may be useful for the simultaneous refining of abinitio calculations and the determination of coupling potentials. For the three-state case, initial guesses differing from the model coupling potentials by as much as ±50% yield successful inversions using either method, therefore indicating that the procedure may be even more useful for the recovery of multiple coupling potentials.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469591
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  • 6
    Electronic Resource
    Electronic Resource
    A new approach to molecular classical optimal control: Application to the reaction HCN→HC+N (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 226-236 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a new method for classical control theory of Hamiltonian systems. This approach is based on a special treatment of the adjoint or Lagrange multiplier equations of motion. The latter function is only asked to preserve the mean of the ensemble of molecular trajectories. In the present case only four such equations are involved greatly simplifying the field design process and making it faster and more stable. Good results are obtained for the selective photodissociation of HCN. The objective is to control the intramolecular reaction HCN→HC+N (i.e., break the stronger bond). Hamilton's equations of motion are employed to model the HCN molecule, initially in its ground state. The control equations are integrated to obtain a high degree of selectivity in the unimolecular dissociation. The robustness of the results to changes in the initial conditions and pulse durations are investigated. An increase of the pulse duration beyond a certain point makes it more difficult to dissociate the N atom due to strong intramolecular coupling. The resultant pulse fields may serve as a basic indicator for future experimental selective dissociation of HCN→HC+N using high power lasers. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469395
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  • 7
    Electronic Resource
    Electronic Resource
    Multicomponent semiconductor material discovery guided by a generalized correlated function expansion (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 10640-10651 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A correlated function expansion (CFE) is presented to systematically sample an N-dimensional dual composition-processing variable space to efficiently guide the laboratory discovery complex materials with desirable properties. The CFE breaks down the material properties in terms of the independent, pair and higher order cooperative roles of the composition-processing variables. The CFE is expected to rapidly converge in the N-dimensional space of variables to specify (1) minimally sized hierarchical libraries of materials, and (2) how to utilize the observed properties of the library members to rapidly estimate the material properties throughout the entire composition-processing variable space. As an illustration the material properties (i.e., alloy bond length and the direct optical band gap E0) over the full composition space of the multicomponent semiconductor alloys, GaxIn1−xPyAs1−y, GaxIn1−xAsySb1−y, and GaxIn1−xPySbzAs1−y−z, are expressed through the CFE in terms of existing ternary experimental data. Band gap experimental results for GaxIn1−xPyAs1−y lattice matched to InP and for GaxIn1−xAsySb1−y lattice matched to GaSb are in good agreement with the CFE estimates from ternary input data alone. The alloy GaxIn1−xPySbzAs1−y−z is found to provide more diverse opportunities to achieve desired band gaps while still maintaining the lattice matching conditions by controlling the concentration of Sb at the anion site. For even broader classes of materials the CFE is generic tool designed to guide laboratory syntheses to aid in the discovery of new materials with desired properties. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.480417
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  • 8
    Electronic Resource
    Electronic Resource
    Potential surfaces from the inversion of time dependent probability density data (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 472-480 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: This article presents an algorithm to assess the feasibility of inverting probability density data to extract potential surfaces. Such data admit the generation of a noniterative quantum inversion algorithm that does not require the solution of the Schrödinger equation. Tikhonov regularization is employed to manage the singular nature of the problem. The inversion in regular regions has excellent accuracy, and an error analysis also indicates that the potential in the regular regions is stable under perturbations from noisy data. The regular regions of the potential are identified by the algorithm. The algorithm does not require knowledge of the excitation process initiating the evolution of the system. Analysis indicates that the most detailed potential surface information will result from broadband excitation leaving the molecule with significant population in as many quantum states as possible. The inversion algorithm is tested in a simulation for the O–H potential, which shows that the algorithm is very fast and reliable. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.479328
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  • 9
    Electronic Resource
    Electronic Resource
    Optimal Control of Electronic Excitation in Molecular Aggregates (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 6789-6793 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100018a006
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  • 10
    Electronic Resource
    Electronic Resource
    Analytical Derivatives of Molecular Vibrational Frequencies with Respect to Coordinates and Model Potential Parameters (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 9344-9351 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100023a008
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