Biomedical subjects

Eitan Geva

Publications and source records attributed to Eitan Geva.

12 recordsLinked to original sources

PubMed2007

Vibrational energy relaxation rates of H2 and D2 in liquid argon via the linearized semiclassical method.

The vibrational energy relaxation (VER) rates for H2 and D2 in liquid argon (T=152 K, rho=1.45x1022 cm-3) are calculated using the linearized semiclassical (LSC) method (J. Phys. Chem. 2003, 107, 9059, 9070). The calculation is based on Fermi's golden rule. The VER rate constant is expressed in terms of the quantum-mechanical force-force correlation function, which is then estimated using the LSC method. A local harmonic approximation (LHA) is employed in order to compute the multidimensional Wigner integrals underlying the LSC approximation. The H2-Ar and D2-Ar interactions are described by the three-body potential of Bissonette et al. (J. Phys. Chem. A 1996, 105, 2639). The LHA-LSC-based VER rate constants for both D2 and H2 are found to be about 2-3 orders of magnitude slower than those obtained experimentally. However, their ratio agrees quantitatively with the corresponding experimental result. In contrast, the classical VER rate constants are found to be 8-9 orders of magnitude slower than those obtained experimentally, and their ratio is found to be qualitatively different from the corresponding experimental result.

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PubMed2006

Classical vs quantum vibrational energy relaxation pathways in solvated polyatomic molecules.

Vibrational energy relaxation (VER) of solvated polyatomic molecules can occur via different pathways. In this paper, we address the question of whether treating VER classically or quantum-mechanically can lead to different predictions with regard to the preferred pathway. To this end, we consider the relaxation of the singly excited asymmetric stretch of a rigid, symmetrical, and linear triatomic molecule (A-B-A) in a monatomic liquid. In this case, VER can occur either directly to the ground state or indirectly via intramolecular vibrational relaxation (IVR) to the symmetric stretch. We have calculated the rates of these two different VER pathways via classical mechanics and the linearized semiclassical (LSC) method. When the mass of the terminal A atoms is significantly larger than that of the central B atom, we find that LSC points to intermolecular VER as the preferred pathway, whereas the classical treatment points to IVR. The origin of this trend reversal appears to be purely quantum-mechanical and can be traced back to the significantly weaker quantum enhancement of solvent-assisted IVR in comparison to that of intermolecular VER.

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PubMed2006

A nonperturbative calculation of nonlinear spectroscopic signals in liquid solution.

Nonlinear spectroscopic signals in liquid solution were calculated without treating the field-matter interaction in a perturbative manner. The calculation is based on the assumption that the intermolecular degrees of freedom can be treated classically, while the time evolution of the electronic state is treated quantum mechanically. The calculated overall electronic polarization is then resolved into its directional components via the method of Seidner et al. [J. Chem. Phys. 103, 3998 (1995)]. It is shown that the time dependence of the directional components is independent of laser intensity in the impulsive pulse regime, which allows for flexibility in choosing the procedure for calculating optical response functions. The utility and robustness of the nonperturbative procedure is demonstrated in the case of a two-state chromophore solvated in a monoatomic liquid, by calculating nonlinear time-domain signals in the strong-field, weak-field, impulsive, and nonimpulsive regimes.

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PubMed2006

Homogeneity and Markovity of electronic dephasing in liquid solutions.

The electronic dephasing dynamics of a solvated chromophore is formulated in terms of a non-Markovian master equation. Within this formulation, one describes the effect of the nuclear degrees of freedom on the electronic degrees of freedom in terms of a memory kernel function, which is explicitly dependent on the initial solvent configuration. In the case of homogeneous dynamics, this memory kernel becomes independent of the initial configuration. The Markovity of the dephasing process is also the most conveniently explored by comparing the results obtained via the non-Markovian master equation to these obtained via its Markovian counterpart. The homogeneous memory kernel is calculated for a two-state chromophore in liquid solution, and used to explore the sensitivity of photon echo signals to the heterogeneity and non-Markovity of the underlying solvation dynamics.

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PubMed2006

Vibrational energy relaxation of polyatomic molecules in liquid solution via the linearized semiclassical method.

Vibrational energy relaxation (VER) of polyatomic, as opposed to diatomic, molecules can occur via different, often solvent assisted, intramolecular and/or intermolecular pathways. In this paper, we apply the linearized semiclassical (LSC) method for calculating VER rates in the prototypical case of a rigid, symmetrical and linear triatomic molecule (A-B-A) in a monatomic liquid. Starting at the first excited state of either the symmetric or asymmetric stretches, VER can occur either directly to the ground state or indirectly via intramolecular vibrational relaxation (IVR). The VER rate constants for the various pathways are calculated within the framework of the Landau-Teller formalism, where they are expressed in terms of two-time quantum-mechanical correlation functions. The latter are calculated by the LHA-LSC method, which puts them in a "Wignerized" form, and employs a local harmonic approximation (LHA) in order to compute the necessary multidimensional Wigner integrals. Results are reported for the LHL/Ar model of Deng and Stratt [J. Chem. Phys. 2002, 117, 1735], as well as for CO(2) in liquid argon and in liquid neon. The LHA-LSC method is shown to give rise to significantly faster VER and IVR rates in comparison to the classical treatment, particularly at lower temperatures. We also find that the type and extent of the quantum rate enhancement is strongly dependent on the particular VER pathway. Finally, we find that the classical and semiclassical treatments can give rise to opposite trends when it comes to the dependence of the VER rates on the solvent.

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PubMed2006

Nonequilibrium quantum dynamics in the condensed phase via the generalized quantum master equation.

The Nakajima-Zwanzig generalized quantum master equation provides a general, and formally exact, prescription for simulating the reduced dynamics of a quantum system coupled to a quantum bath. In this equation, the memory kernel accounts for the influence of the bath on the system's dynamics, and the inhomogeneous term accounts for initial system-bath correlations. In this paper, we propose a new approach for calculating the memory kernel and inhomogeneous term for arbitrary initial state and system-bath coupling. The memory kernel and inhomogeneous term are obtained by numerically solving a single inhomogeneous Volterra equation of the second kind for each. The new approach can accommodate a very wide range of projection operators, and requires projection-free two-time correlation functions as input. An application to the case of a two-state system with diagonal coupling to an arbitrary bath is described in detail. Finally, the utility and self-consistency of the formalism are demonstrated by an explicit calculation on a spin-boson model.

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PubMed2005

A computational study of the correlations between structure and dynamics in free and surface-immobilized single polymer chains.

The correlations between structure and dynamics in free and surface-immobilized polymers were investigated via Langevin dynamics simulations of a free-jointed homopolymer. A detailed analysis was performed for a polymer in free solution and a polymer attached to a surface. The cases of repulsive and attractive surfaces, as well as poor and good solvents, were considered. The analysis focuses on properties that are particularly relevant to single molecule measurements, namely: (1) the distribution of end-to-end distance, (2) the correlations between the conformational structure and the time scale of its motion, (3) the correlations, at equilibrium, between the end-to-end distance and its displacement, and (4) the correlation between the initial coil conformation and the collapse pathway into the globular state. The differences and similarities between this model and a previously considered model of a protein, with two-state folding kinetics and a well-defined native state, are also discussed.

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PubMed2005

Vibrational energy relaxation rates via the linearized semiclassical approximation: applications to neat diatomic liquids and atomic-diatomic liquid mixtures.

We report the results obtained from the application of our previously proposed linearized semiclassical method for computing vibrational energy relaxation (VER) rates (J. Phys. Chem. A 2003, 107, 9059, 9070) to neat liquid oxygen, neat liquid nitrogen, and liquid mixtures of oxygen and argon. Our calculations are based on a semiclassical approximation for the quantum-mechanical force-force correlation function, which puts it in terms of the Wigner transforms of the force and the product of the Boltzmann operator and the force. The calculation of the multidimensional Wigner integrals is made feasible by the introduction of a local harmonic approximation. A systematic analysis has been performed of the temperature and mole-fraction dependences of the VER rate constant, as well as the relative contributions of centrifugal and potential forces, and of different types of quantum effects. The results were found to be in very good quantitative agreement with experiment, and they suggest that this semiclassical approximation can capture the quantum enhancement, by many orders of magnitude, of the experimentally observed VER rate constants over the corresponding classical predictions.

Algorithms↗

PubMed2005

A comparison between different semiclassical approximations for optical response functions in nonpolar liquid solutions.

The temporal behavior of optical response functions (ORFs) reflects the quantum dynamics of an electronic superposition state, and as such lacks a well-defined classical limit. In this paper, we consider the importance of accounting for the quantum nature of the dynamics when calculating ORFs of different types. To this end, we calculated the ORFs associated with the linear absorption spectrum and the nonlinear two-pulse photon-echo experiment, via the following approaches: (1) the semiclassical forward-backward approach; (2) an approach based on linearizing the path-integral forward-backward action in terms of the difference between the forward and backward paths; (3) an approach based on ground state nuclear dynamics. The calculations were performed on a model that consists of a two-state chromophore solvated in a nonpolar liquid. The different methods were found to yield very similar results for the absorption spectrum and "diagonal" two-pulse photon echo (i.e., the homodyne-detected signal at time t=t(0) after the second pulse, where t(0) is the time interval between the two pulses). The different approximations yielded somewhat different results in the case of the time-integrated photon-echo signal. The reasons for the similarity between the predictions of different approximations are also discussed.

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PubMed2005

Protein structure and dynamics from single-molecule fluorescence resonance energy transfer.

The pros and cons of single-molecule vs ensemble-averaged fluorescence resonance energy transfer (FRET) experiments, performed on proteins, are explored with the help of Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined native state and two-state folding kinetics. A detailed analysis of the distribution of the donor-acceptor distance is presented at different points along the denaturation curve, along with its dependence on the averaging time window. We show that unique information on the correlation between structure and dynamics, which can only be obtained from single-molecule experiments, is contained in the correlation between the donor-acceptor distance and its displacement. The latter is shown to provide useful information on the free energy landscape of the protein, which is complementary to that obtained from the distribution of donor-acceptor distances.

Fluorescence Resonance Energy Transfer↗

PubMed2004

A derivation of the mixed quantum-classical Liouville equation from the influence functional formalism.

We show that the mixed quantum-classical Liouville equation is equivalent to linearizing the forward-backward action in the influence functional. Derivations are provided in terms of either the diabatic or adiabatic basis sets. An application of the mixed quantum-classical Liouville equation for calculating the memory kernel of the generalized quantum master equation is also presented. The accuracy and computational feasibility of such an approach is demonstrated in the case of a two-level system nonlinearly coupled to an anharmonic bath.

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PubMed2004

A semiclassical generalized quantum master equation for an arbitrary system-bath coupling.

The Nakajima-Zwanzig generalized quantum master equation (GQME) provides a general, and formally exact, prescription for simulating the reduced dynamics of a quantum system coupled to a, possibly anharmonic, quantum bath. In this equation, a memory kernel superoperator accounts for the influence of the bath on the dynamics of the system. In a previous paper [Q. Shi and E. Geva, J. Chem. Phys. 119, 12045 (2003)] we proposed a new approach to calculating the memory kernel, in the case of arbitrary system-bath coupling. Within this approach, the memory kernel is obtained by solving a set of two integral equations, which requires a new type of two-time system-dependent bath correlation functions as input. In the present paper, we consider the application of the linearized semiclassical (LSC) approximation for calculating those correlation functions, and subsequently the memory kernel. The new approach is tested on a benchmark spin-boson model. Application of the LSC approximation for calculating the relatively short-lived memory kernel, followed by a numerically exact solution of the GQME, is found to provide an accurate description of the relaxation dynamics. The success of the proposed LSC-GQME methodology is contrasted with the failure of both the direct application of the LSC approximation and the weak coupling treatment to provide an accurate description of the dynamics, for the same model, except at very short times. The feasibility of the new methodology to anharmonic systems is also demonstrated in the case of a two level system coupled to a chain of Lennard-Jones atoms.

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