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  • Opus Repository ZIB  (334)
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  • 1
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    Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of RamanSpectroscopy. (1992)
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    Publication Date: 2014-02-26
    Description: Models for occupation dynamics in discrete quantum systems lead to large or even infinite systems of ordinary differential equations. Some new mathematical techniques, developed for the simulation of chemical processes, make a numerical solution of countable systems of ordinary differential equations possible. Both, a basic physical concept for the construction of such systems and the structure of the numerical tools for solving them are presented. These conceptual aspects are illustrated by a simulation of an occupation process from spectroscopy. In this example the structures of rotation spectra observed in infrared spectroscopy are explained and some possibilities for an extension of the model are shown.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/pdf
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  • 2
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    Smoothed Molecular Dynamics for Thermally Embedded Systems (1995)
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    Publication Date: 2014-02-26
    Description: This paper makes use of statistical mechanics in order to construct effective potentials for Molecular Dynamics for systems with nonstationary thermal embedding. The usual approach requires the computation of a statistical ensemble of trajectories. In the context of the new model the evaluation of only one single trajectory is sufficient for the determination of all interesting quantities, which leads to an enormous reduction of computational effort. This single trajectory is the solution to a corrected Hamiltonian system with a new potential $\tilde{V}$. It turns out that $\tilde{V}$ can be defined as spatial average of the original potential $V$. Therefore, the Hamiltonian dynamics defined by $\tilde{V}$ is smoother than that effected by $V$, i.e. a numerical integration of its evolution in time allows larger stepsizes. Thus, the presented approach introduces a Molecular Dynamics with smoothed trajectories originating from spatial averaging. This is deeply connected to time--averaging in Molecular Dynamics. These two types of {\em smoothed Molecular Dynamics} share advantages (gain in efficiency, reduction of error amplification, increased stability) and problems (necessity of closing relations and adaptive control schemes) which will be explained in detail.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 3
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    Computation of Essential Molecular Dynamics by Subdivision Techniques I: Basic Concept (1996)
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    Publication Date: 2014-02-26
    Description: The paper presents the concept of a new type of algorithm for the numerical computation of what the authors call the {\em essential dynamics\/} of molecular systems. Mathematically speaking, such systems are described by Hamiltonian differential equations. In the bulk of applications, individual trajectories are of no specific interest. Rather, time averages of physical observables or relaxation times of conformational changes need to be actually computed. In the language of dynamical systems, such information is contained in the natural invariant measure (infinite relaxation time) or in almost invariant sets ("large" finite relaxation times). The paper suggests the direct computation of these objects via eigenmodes of the associated Frobenius-Perron operator by means of a multilevel subdivision algorithm. The advocated approach is different to both Monte-Carlo techniques on the one hand and long term trajectory simulation on the other hand: in our setup long term trajectories are replaced by short term sub-trajectories, Monte-Carlo techniques are just structurally connected via the underlying Frobenius-Perron theory. Numerical experiments with a first version of our suggested algorithm are included to illustrate certain distinguishing properties. A more advanced version of the algorithm will be presented in a second part of this paper.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 4
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    Chebyshev-Approximation for Wavepacket-Dynamics: better than expected (1996)
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    Publication Date: 2014-02-26
    Description: The aim of this work is to study the accuracy and stability of the Chebyshev--approximation method as a time--discretization for wavepacket dynamics. For this frequently used discretization we introduce estimates of the approximation and round--off error. These estimates mathematically confirm the stability of the Chebyshev--approximation with respect to round--off errors, especially for very large stepsizes. But the results also disclose threads to the stability due to large spatial dimensions. All theoretical statements are illustrated by numerical simulations of an analytically solvable example, the harmonic quantum oszillator.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 5
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    On the Singular Limit of the Quantum-Classical Molecular Dynamics Model (1997)
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    Publication Date: 2014-02-26
    Description: \noindent In molecular dynamics applications there is a growing interest in so-called {\em mixed quantum-classical} models. These models describe most atoms of the molecular system by the means of classical mechanics but an important, small portion of the system by the means of quantum mechanics. A particularly extensively used model, the QCMD model, consists of a {\em singularly perturbed}\/ Schrödinger equation nonlinearly coupled to a classical Newtonian equation of motion. This paper studies the singular limit of the QCMD model for finite dimensional Hilbert spaces. The main result states that this limit is given by the time-dependent Born-Oppenheimer model of quantum theory---provided the Hamiltonian under consideration has a smooth spectral decomposition. This result is strongly related to the {\em quantum adiabatic theorem}. The proof uses the method of {\em weak convergence} by directly discussing the density matrix instead of the wave functions. This technique avoids the discussion of highly oscillatory phases. On the other hand, the limit of the QCMD model is of a different nature if the spectral decomposition of the Hamiltonian happens not to be smooth. We will present a generic example for which the limit set is not a unique trajectory of a limit dynamical system but rather a {\em funnel} consisting of infinitely many trajectories.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 6
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    Partial Wigner Transforms and the Quantum--Classical Liouville Equation (1999)
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    Publication Date: 2014-02-26
    Description: In molecular dynamics applications there is a growing interest in mixed quantum-classical models. The {\em quantum-classical Liouville equation} (QCL) describes most atoms of the molecular system under consideration by means of classical phase space density but an important, small portion of the system by means of quantum mechanics. The QCL is derived from the full quantum dynamical (QD) description by applying the Wigner transform to the classical part'' of the system only. We discuss the conditions under which the QCL model approximates the full QD evolution of the system. First, analysis of the asymptotic properties of the Wigner transform shows that solving the QCL yields a first order approximation of full quantum dynamics. Second, we discuss the adiabatic limit of the QCL. This discussion shows that the QCL solutions may be interpretated as classical phase space densities, at least near the adiabatic limit. Third, it is demonstrated that the QCL yields good approximations of {\em non-adiabatic quantum effects,} especially near so-called {\em avoided crossings} where most quantum-classical models fail.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
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  • 7
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    From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods (1998)
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    Publication Date: 2014-02-26
    Description: Statistical methods for analyzing large data sets of molecular configurations within the chemical concept of molecular conformations are described. The strategies are based on dependencies between configurations of a molecular ensemble; the article concentrates on dependencies induces by a) correlations between the molecular degrees of freedom, b) geometrical similarities of configurations, and c) dynamical relations between subsets of configurations. The statistical technique realizing aspect a) is based on an approach suggested by {\sc Amadei et al.} (Proteins, 17 (1993)). It allows to identify essential degrees of freedom of a molecular system and is extended in order to determine single configurations as representatives for the crucial features related to these essential degrees of freedom. Aspects b) and c) are based on statistical cluster methods. They lead to a decomposition of the available simulation data into {\em conformational ensembles} or {\em subsets} with the property that all configurations in one of these subsets share a common chemical property. In contrast to the restriction to single representative conformations, conformational ensembles include information about, e.g., structural flexibility or dynamical connectivity. The conceptual similarities and differences of the three approaches are discussed in detail and are illustrated by application to simulation data originating from a hybrid Monte Carlo sampling of a triribonucleotide.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 8
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    A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo (1999)
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    Publication Date: 2014-02-26
    Description: Recently, a novel concept for the computation of essential features of the dynamics of Hamiltonian systems (such as molecular dynamics) has been proposed. The realization of this concept had been based on subdivision techniques applied to the Frobenius--Perron operator for the dynamical system. The present paper suggests an alternative but related concept that merges the conceptual advantages of the dynamical systems approach with the appropriate statistical physics framework. This approach allows to define the phrase ``conformation'' in terms of the dynamical behavior of the molecular system and to characterize the dynamical stability of conformations. In a first step, the frequency of conformational changes is characterized in statistical terms leading to the definition of some Markov operator $T$ that describes the corresponding transition probabilities within the canonical ensemble. In a second step, a discretization of $T$ via specific hybrid Monte Carlo techniques is shown to lead to a stochastic matrix $P$. With these theoretical preparations, an identification algorithm for conformations is applicable. It is demonstrated that the discretization of $T$ can be restricted to few essential degrees of freedom so that the combinatorial explosion of discretization boxes is prevented and biomolecular systems can be attacked. Numerical results for the n-pentane molecule and the triribonucleotide adenylyl\emph{(3'-5')}cytidylyl\emph{(3'-5')}cytidin are given and interpreted.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 9
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    On Conformational Dynamics induced by Langevin Processes (1999)
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    Publication Date: 2014-02-26
    Description: The function of many important biomolecules is related to their dynamic properties and their ability to switch between different {\em conformations}, which are understood as {\em almost invariant} or {\em metastable} subsets of the positional state space of the system. Recently, the present authors and their coworkers presented a novel algorithmic scheme for the direct numerical determination of such metastable subsets and the transition probability between them. Although being different in most aspects, this method exploits the same basic idea as {\sc Dellnitz} and {\sc Junge} in their approach to almost invariance in discrete dynamical systems: the almost invariant sets are computed via certain eigenvectors of the Markov operators associated with the dynamical behavior. In the present article we analyze the application of this approach to (high--friction) Langevin models describing the dynamical behavior of molecular systems coupled to a heat bath. We will see that this can be related to theoretical results for (symmetric) semigroups of Markov operators going back to {\sc Davies}. We concentrate on a comparison of our approach in respect to random perturbations of dynamical systems.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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  • 10
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    A Quasiresonant Smoothing Algorithm for Solving Large Highly Differential Equations from Quantum Chemistry. (1994)
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    Publication Date: 2014-02-27
    Description: In Quantum Chemistry the field of Laser--Assisted Molecular Control'' has received a considerable amount of attention recently. One key problem in this new field is the simulation of the dynamical reaction of a molecule subjected to external radiation. This problem is described by the Schrödinger equation, which, after eigenfunction expansion, can be written in the form of a large system of ordinary differential equations, the solutions of which show a highly oscillatory behaviour. The oscillations with high frequencies and small amplitudes confine the stepsizes of any numerical integrator -- an effect, which, in turn, blows up the simulation time. Larger stepsizes can be expected by averaging these fast oscillations, thus smoothing the trajectories. Standard smoothing techniques (averaging, filtering) would kill the whole process and thus, lead to wrong numerical results. To avoid this unwanted effect and nevertheless speed up computations, this paper presents a quasiresonant smoothing algorithm (QRS). In QRS, a natural splitting parameter $\delta$ controls the smoothing properties. An adaptive QRS--version (AQRS) is presented which includes an error estimation scheme for choosing this parameter $\delta$ in order to meet a given accuracy requirement. In AQRS $\delta$ is permanently adapted to the solution properties for computing the chemically necessary information'' only. The performance of AQRS is demonstrated in several test problems from the field Laser--Assisted Selective Excitation of Molecules'' in which the external radiation is a picosecond laser pulse. In comparison with standard methods speedup factors of the order of $10^2$ are observed.
    Keywords: ddc:000
    Language: English
    Type: doctoralthesis , doc-type:doctoralThesis
    Format: application/postscript
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