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Biomedical subjects

Peter Saalfrank

Publications and source records attributed to Peter Saalfrank.

9 recordsLinked to original sources
PubMed2006

A local coherent-state approximation to system-bath quantum dynamics.

A novel quantum method to deal with typical system-bath dynamical problems is introduced. Subsystem discrete variable representation and bath coherent-state sets are used to write down a multiconfigurational expansion of the wave function of the whole system. With the help of the Dirac-Frenkel variational principle, simple equations of motion--a kind of Schrodinger-Langevin equation for the subsystem coupled to (pseudo) classical equations for the bath--are derived. True dissipative dynamics at all times is obtained by coupling the bath to a secondary, classical Ohmic bath, which is modeled by adding a friction coefficient in the derived pseudoclassical bath equations. The resulting equations are then solved for a number of model problems, ranging from tunneling to vibrational relaxation dynamics. Comparison of the results with those of exact, multiconfiguration time-dependent Hartree calculations in systems with up to 80 bath oscillators shows that the proposed method can be very accurate and might be of help in studying realistic problems with very large baths. To this end, its linear scaling behavior with respect to the number of bath degrees of freedom is shown in practice with model calculations using tens of thousands of bath oscillators.

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PubMed2006

On the electronic structure of neutral and ionic azobenzenes and their possible role as surface mounted molecular switches.

We report quantum chemical calculations, mostly based on density functional theory, on azobenzene and substituted azobenzenes as neutral molecules or ions, in ground and excited states. Both the cis and trans configurations are computed as well as the activation energies to transform one isomer into the other and the possible reaction paths and reaction surfaces along the torsion and inversion modes. All calculations are done for the isolated species, but results are discussed in light of recent experiments aiming at the switching of surface mounted azobenzenes by scanning tunneling microscopes.

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PubMed2006

Optimal control in a dissipative system: vibrational excitation of CO/Cu(100) by IR pulses.

The question as to whether state-selective population of molecular vibrational levels by shaped infrared laser pulses is possible in a condensed phase environment is of central importance for such diverse fields as time-resolved spectroscopy, quantum computing, or "vibrationally mediated chemistry." This question is addressed here for a model system, representing carbon monoxide adsorbed on a Cu(100) surface. Three of the six vibrational modes are considered explicitly, namely, the CO stretch vibration, the CO-surface vibration, and a frustrated translation. Optimized infrared pulses for state-selective excitation of "bright" and "dark" vibrational levels are designed by optimal control theory in the framework of a Markovian open-system density matrix approach, with energy flow to substrate electrons and phonons, phase relaxation, and finite temperature accounted for. The pulses are analyzed by their Husimi "quasiprobability" distribution in time-energy space.

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PubMed2006

Theoretical study of vibration-phonon coupling of H adsorbed on a Si(100) surface.

In this paper a perturbation-theory study of vibrational lifetimes for the bending and stretching modes of hydrogen adsorbed on a Si(100) surface is presented. The hydrogen-silicon interaction is treated with a semiempirical bond-order potential. Calculations are performed for H-Si clusters of different sizes. The finite lifetime is due to vibration-phonon coupling, which is assumed to be linear or bilinear in the phonon and nonlinear in the H-Si stretching and bending modes. Lifetimes and vibrational transition rates are evaluated with one- and two-phonon processes taken into account. Temperature effects are also discussed. In agreement with the experiment and previous theoretical treatment it is found that the H-Si (upsilon(s) = 1) stretching vibration decays on a nanosecond timescale, whereas for the H-Si (upsilon(b) = 1) bending mode a picosecond decay is predicted. For higher-excited vibrations, simple scaling laws are found if the excitation energies are not too large. The relaxation mechanisms for the excited H-Si stretching and the H-Si bending modes are analyzed in detail.

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PubMed2005

Time-dependent configuration-interaction calculations of laser-pulse-driven many-electron dynamics: controlled dipole switching in lithium cyanide.

We report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (doubles) approach. The method accounts for the correlation of ground and excited states, is capable of describing explicitly time-dependent, nonlinear phenomena, and is systematically improvable. Lithium cyanide serves as a molecular test system in which the charge distribution and hence the dipole moment are shown to be switchable, in a controlled fashion, by (a series of) laser pulses which induce selective, state-to-state electronic transitions. One focus of our time-dependent calculations is the question of how fast the transition from the ionic ground state to a specific excited state that is embedded in a multitude of other states can be made, without creating an electronic wave packet.

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PubMed2003

Ab initio quantum chemical investigation of the first steps of the photocycle of phototropin: a model study.

Phototropin is a blue light-activated photoreceptor that plays a dominant role in the phototropism of plants. The protein contains two subunits that bind flavin mononucleotide (FMN), which are responsible for the initial steps of the light-induced reaction. It has been proposed that the photoexcited flavin molecule adds a cysteine residue of the protein backbone, thus activating autophosphorylation of the enzyme. In this study, the electronic properties of several FMN-related compounds in different charge and spin states are characterized by means of ab initio quantum mechanical calculations. The model compounds serve as idealized model chromophores for phototropism. Reaction energies are estimated for simple model reactions, roughly representing the addition of a cysteine residue to the flavin molecule. Excitation energies were calculated with the help of time-dependent density functional theory. On the basis of these calculations we propose the following mechanism for the addition reaction: (1) after photoexcitation of FMN out of the singlet ground state S0, excited singlet state(s) are populated; these relax to the lowest excited singlet state S1, and subsequently by intersystem crossing FMN in the lowest triplet state, T1 is formed; (2) the triplet easily removes the neutral hydrogen atom from the H-S group of the cysteine residue; and (3) the resulting thio radical is added.

Cryptochromes↗
PubMedDate not supplied

Molecular dynamics simulation of the LOV2 domain from Adiantum capillus-veneris.

The mechanism for signal transduction from the LOV-domains toward the kinase region of phototropin is still not well understood. We have performed molecular dynamics (MD) simulations and CONCOORD calculations on the LOV2 domain of Adiantum capillus-veneris, with the goal to detect possible differences between the two forms of the LOV domain which may not show up in the static crystal structures. Since no such clear differences are found in the MD simulations also, we suggest that the real, biologically active conformation of the LOV domain within the whole phototropin is different from the crystal structure of the isolated LOV domains. The MD simulations do offer, however, insight into details of the dynamics of the dark and illuminated LOV domains, which are discussed in the light of recent experiments.

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