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Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches.

ABSTRACT: Our general framework for the simulation of vibrational signatures in electronic spectra has been extended to treat one large-amplitude motion (LAM) at the anharmonic level, coupled to the other small-amplitude motions (SAM) treated as harmonic. The coupling between LAM and SAM is minimized thanks to the use of delocalized internal coordinates, which are built automatically from the molecular topology. General LAMs can be employed, ranging from intrinsic reaction coordinates to rigid or flexible paths based on the distinguished coordinate approach. The anharmonic model is based on a fully numerical method based on the discrete variable representation (DVR) theory, supporting different types of boundary conditions. The inclusion of this model in a general-purpose electronic structure code makes available to the user a large panel of quantum chemistry models, for both isolated and condensed phases. The flexibility and reliability of the new framework are illustrated by some case studies, covering various types of LAMs, ranging from a small test case, the photoelectron spectrum of ammonia, to larger systems, such as phenylanthracene and cyclobutanone.

SUBMITTER: Baiardi A

PROVIDER: S-EPMC5732573 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches.

Baiardi Alberto A Bloino Julien J Barone Vincenzo V

Journal of chemical theory and computation 20170602 6

Our general framework for the simulation of vibrational signatures in electronic spectra has been extended to treat one large-amplitude motion (LAM) at the anharmonic level, coupled to the other small-amplitude motions (SAM) treated as harmonic. The coupling between LAM and SAM is minimized thanks to the use of delocalized internal coordinates, which are built automatically from the molecular topology. General LAMs can be employed, ranging from intrinsic reaction coordinates to rigid or flexible ...[more]

PMID: 28467703

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Project description:BackgroundSimulation-based training allows trainees to experiment during training and end-of-training tests could increase motivation and retention. The aim of this trial was to determine if a simulation-based training program including directed self-regulated learning and post-testing improved clinical outcomes compared to a traditional simulation-based training program.MethodsA randomized trial was conducted involving 32 participants without prior experience in endoscopic procedures. The intervention group practiced independently in a simulation centre and got a post-test whereas the control group received traditional instructions and demonstrations before being allowed to practice. Three weeks after the intervention the participants performed cystoscopies on two consecutive patients. Clinical performance was assessed using a global rating scale (GRS) with established evidence of validity. Independent samples t-test, Cronbach's α, Pearson's r, and paired samples t-test were used for statistical analysis.ResultsTwenty-five participants performed two cystoscopies on patients. There was no significant difference between the two study groups with respect to mean GRS of performance (p = 0.63, 95 % CI; -2.4-3.9). The internal consistency of the global rating scale was high, Cronbach's α = 0.91. Participants from both study groups demonstrated significant improvement between the first and second clinical procedures (p = 0.004, 95 % CI, 0.8-3.5). Eight (32%) and 15 (60%) participants demonstrated adequate clinical skills in their first and second procedure, respectively.ConclusionsNo significant differences were found on the clinical transfer when comparing the two programs. Neither of our training programs was able to ensure consistent, competent performance on patients and this finding could serve as an important argument for simulation-based mastery learning where all training continues until a pre-defined level of proficiency is met.Trial registrationsThe trial was submitted before enrolment of participants to the Regional Scientific Ethics Committee of the Capital Region which established that ethical approval was not necessary (H-4-2014-122). The trial was registered at Clinicaltrials.gov (NCT02411747).

Project description:Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.

Dataset Information

Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches.

Publications

Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches.

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