Biomedical subjects

Ahren W Jasper

Publications and source records attributed to Ahren W Jasper.

10 recordsLinked to original sources

PubMed2006

Phase behavior of elemental aluminum using monte carlo simulations.

Monte Carlo simulations are presented for two models of aluminum: an embedded-atom model and an explicit many-body model. Vapor/liquid coexistence curves are determined using Gibbs ensemble Monte Carlo simulations. The normal boiling points predicted by both models are somewhat higher (by about 10%) than the experimental value. Isothermal constant-stress simulations are used to simulate solid Al from 300 K to the triple point. The solid structures are at least metastable in the face-centered cubic configuration, and the specific heat is determined to be lower than the experimental value. The melting point for the embedded-atom model determined via thermodynamic integration along a pseudo-supercritical path is approximately 20% higher than the experimental value.

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PubMed2006

Critical properties of aluminum.

Gibbs ensemble Monte Carlo calculations are performed using a validated embedded-atom potential to obtain the vapor-liquid coexistence curve for elemental aluminum in good agreement with available experimental data up to the boiling point. These calculations are then extended to make a reliable prediction of the critical temperature, pressure, and density of Al, which have previously been known only with very large uncertainties. This demonstrates the ability of modern simulations to predict fundamental physical properties that are extremely difficult to measure directly.

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PubMed2006

Non-Born-Oppenheimer molecular dynamics.

Electronically nonadiabatic or non-Born-Oppenheimer (non-BO) chemical processes (photodissociation, charge-transfer, etc.) involve a nonradiative change in the electronic state of the system. Molecular dynamics simulations typically treat nuclei as moving classically on a single adiabatic potential energy surface, and these techniques are not immediately generalizable to non-BO systems due to the inherently quantum mechanical nature of electronic transitions. Here we generalize the concept of a single-surface molecular dynamics trajectory to that of a coupled-surface non-BO trajectory that evolves "semiclassically" under the influence of two or more electronic states and their couplings. Five non-BO trajectory methods are discussed. Next, we summarize the results of a series of systematic studies using a database of accurate quantum mechanical reaction probabilities and internal energy distributions for several six-dimensional model bimolecular scattering collisions. The test set includes three kinds of prototypical nonadiabatic interactions: conical intersections, avoided crossings, and regions of weak coupling. We show that the coherent switching with decay of mixing (CSDM) non-BO trajectory method provides a robust and accurate way to extend molecular dynamics to treat electronically nonadiabatic chemistry for all three kinds of nonadiabatic interactions, and we recommend it for molecular dynamics simulations involving nonradiative electronic state changes.

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PubMed2005

Electronic decoherence time for non-Born-Oppenheimer trajectories.

An expression is obtained for the electronic decoherence time of the reduced density electronic matrix in mixed quantum-classical molecular-dynamics simulations. The result is obtained by assuming that decoherence is dominated by the time dependence of the overlap of minimum-uncertainty packets and then maximizing the rate with respect to the parameters of the wave packets. The expression for the decay time involves quantities readily available in non-Born-Oppenheimer molecular-dynamics simulations, and it is shown to have a reasonable form when compared with two other formulas for the decay time that have been previously proposed.

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PubMed2005

Analytic potential energy functions for simulating aluminum nanoparticles.

Potential energy functions (PEFs) parametrized to bulk data are shown to perform poorly for small aluminum nanoparticles and clusters. In contrast, PEFs parametrized to a limited set of cluster and bulk data, but no nanoparticle data, perform well for nanoparticles. This validates a practical scheme for developing PEFs for nanoscale systems. Building on these findings, we optimized five PEFs by minimizing the error in the fit over a broad data set. Two of these PEFs have errors of less than or equal to 0.08 eV/atom for each of three categories of system sizes, i.e., for small clusters, for nanoparticles, and for bulk potential energies.

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PubMed2005

Conical intersections and semiclassical trajectories: comparison to accurate quantum dynamics and analyses of the trajectories.

Semiclassical trajectory methods are tested for electronically nonadiabatic systems with conical intersections. Five triatomic model systems are presented, and each system features two electronic states that intersect via a seam of conical intersections (CIs). Fully converged, full-dimensional quantum mechanical scattering calculations are carried out for all five systems at energies that allow for electronic de-excitation via the seam of CIs. Several semiclassical trajectory methods are tested against the accurate quantum mechanical results. For four of the five model systems, the diabatic representation is the preferred (most accurate) representation for semiclassical trajectories, as correctly predicted by the Calaveras County criterion. Four surface hopping methods are tested and have overall relative errors of 40%-60%. The semiclassical Ehrenfest method has an overall error of 66%, and the self-consistent decay of mixing (SCDM) and coherent switches with decay of mixing (CSDM) methods are the most accurate methods overall with relative errors of approximately 32%. Furthermore, the CSDM method is less representation dependent than both the SCDM and the surface hopping methods, making it the preferred semiclassical trajectory method. Finally, the behavior of semiclassical trajectories near conical intersections is discussed.

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PubMed2004

Coherent switching with decay of mixing: an improved treatment of electronic coherence for non-Born-Oppenheimer trajectories.

The self-consistent decay-of-mixing (SCDM) semiclassical trajectory method for electronically nonadiabatic dynamics is improved by modifying the switching probability that determines the instantaneous electronic state toward which the system decoheres. This method is called coherent switching with decay of mixing (CSDM), and it differs from the previously presented SCDM method in that the electronic amplitudes controlling the switching of the decoherent state are treated fully coherently in the electronic equations of motion for each complete passage through a strong interaction region. It is tested against accurate quantum mechanical calculations for 12 atom-diatom scattering test cases. Also tested are the SCDM method and the trajectory surface hopping method of Parlant and Gislason that requires coherent passages through each strong interaction region, and which we call the "exact complete passage" trajectory surface hopping (ECP-TSH) method. The results are compared with previously presented results for the fewest switches with time uncertainty and Tully's fewest switches (TFS) surface hopping methods and the semiclassical Ehrenfest method. We find that the CSDM method is the most accurate of the semiclassical trajectory methods tested. Including coherent passages improves the accuracy of the SCDM method (i.e., the CSDM method is more accurate than the SCDM method) but not of the trajectory surface hopping method (i.e., the ECP-TSH method is not more accurate on average than the TFS method).

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PubMed2004

Non-Born-Oppenheimer trajectories with self-consistent decay of mixing.

A semiclassical trajectory method, called the self-consistent decay of mixing (SCDM) method, is presented for the treatment of electronically nonadiabatic dynamics. The SCDM method is a modification of the semiclassical Ehrenfest (SE) method (also called the semiclassical time-dependent self-consistent-field method) that solves the problem of unphysical mixed final states by including decay-of-mixing terms in the equations for the evolution of the electronic state populations. These terms generate a force, called the decoherent force (or dephasing force), that drives the electronic component of each trajectory toward a pure state. Results for several mixed quantum-classical methods, in particular the SCDM, SE, and natural-decay-of-mixing methods and several trajectory surface hopping methods, are compared to the results of accurate quantum mechanical calculations for 12 cases involving five different fully dimensional triatomic model systems. The SCDM method is found to be the most accurate of the methods tested. The method should be useful for the simulation of photochemical reactions.

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PubMed2004

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method.

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

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PubMed2004

Introductory lecture: nonadiabatic effects in chemical dynamics.

Recent progress in the theoretical treatment of electronically nonadiabatic processes is discussed. First we discuss the generalized Born-Oppenheimer approximation, which identifies a subset of strongly coupled states, and the relative advantages and disadvantages of adiabatic and diabatic representations of the coupled surfaces and their interactions are considered. Ab initio diabatic representations that do not require tracking geometric phases or calculating singular nonadiabatic nuclear momentum coupling will be presented as one promising approach for characterizing the coupled electronic states of polyatomic photochemical systems. Such representations can be accomplished by methods based on functionals of the adiabatic electronic density matrix and the identification of reference orbitals for use in an overlap criterion. Next, four approaches to calculating or modeling electronically nonadiabatic dynamics are discussed: (1) accurate quantum mechanical scattering calculations, (2) approximate wave packet methods, (3) surface hopping, and (4) self-consistent-potential semiclassical approaches. The last two of these are particularly useful for polyatomic photochemistry, and recent refinements of these approaches will be discussed. For example, considerable progress has been achieved in making the surface hopping method more applicable to the study of systems with weakly coupled electronic states. This includes introducing uncertainty principle considerations to alleviate the problem of classically forbidden surface hops and the development of an efficient sampling algorithm for low-probability events. A topic whose central importance in a number of quantum mechanical fields is becoming more widely appreciated is the introduction of decoherence into the quantal degrees of freedom to account for the effect of the classical treatment on the other degrees of freedom, and we discuss how the introduction of such decoherence into a self-consistent-potential approximation leads to a reasonably accurate but very practical trajectory method for electronically nonadiabatic processes. Finally, the performances of several dynamical methods for Landau-Zener-type and Rosen-Zener-Demkov-type reactive scattering problems are compared.

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