Graphics processing units accelerated semiclassical initial value representation molecular dynamics

Tamascelli, Dario; Dambrosio, Francesco Saverio; Conte, Riccardo; Ceotto, Michele

doi:10.1063/1.4873137

Cited by 33 publications

(37 citation statements)

References 92 publications

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“…A potential drawback related to the width of the peaks is that it may hinder the resolution of spectral features very close to each other. A practical way to overcome this issue, that is largely adopted in semiclassical dynamics, consists in employing a proper combination of coherent states able to introduce a parity symmetry [77,92] which permits to distinguish among spectral features belonging to different vibrational modes. A known issue of semiclassical spectra is represented by the so-called "ghost" peaks.…”

Section: Discussionmentioning

confidence: 99%

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“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

Liberto

Conte

Ceotto

2018

The Journal of Chemical Physics

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100

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We extensively describe our recently established "divide-and-conquer" semiclassical method [M. Ceotto, G. Di Liberto and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)] and propose a new implementation of it to increase the accuracy of results. The technique permits to perform spectroscopic calculations of high dimensional systems by dividing the full-dimensional problem into a set of smaller dimensional ones. The partition procedure, originally based on a dynamical analysis of the Hessian matrix, is here more rigorously achieved through a hierarchical subspace-separation criterion based on Liouville's theorem. Comparisons of calculated vibrational frequencies to exact quantum ones for a set of molecules including benzene show that the new implementation performs better than the original one and that, on average, the loss in accuracy with respect to full-dimensional semiclassical calculations is reduced to only 10 wavenumbers. Furthermore, by investigating the challenging Zundel cation, we also demonstrate that the "divide-and-conquer" approach allows to deal with complex strongly anharmonic molecular systems. Overall the method very much helps the assignment and physical interpretation of experimental IR spectra by providing accurate vibrational fundamentals and overtones decomposed into reduced dimensionality spectra.

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Section: Discussionmentioning

confidence: 99%

“…[76,77,92,93] To further reduce the computational effort, the multiple coherent time averaged SCIVR (MC SCIVR) has been introduced. [58][59][60][61][62]94] In this Section we provide a more detailed explanation of the "divide-and-conquer" strategy previously introduced elsewhere.…”

Section: A Divide and Conquer Strategy For Semiclassical Dynamicsmentioning

confidence: 99%

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

Liberto

Conte

Ceotto

2018

The Journal of Chemical Physics

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100

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“…57,58 In particular, of relevance for the present work is the multiple-coherent time-averaged semiclassical initial value representation (MC-TA-SCIVR), which permits accurate reproduction of molecular vibrational spectra by employing a tailored reference state and a few or even just a single classical trajectory. 59−64 …”

Section: Introductionmentioning

confidence: 99%

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

Gabas

Conte

Ceotto

2017

J. Chem. Theory Comput.

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We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.

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“…A large number of models developed so far occur in 2D, which is suitable for many applications without being too computationally intensive. However, improvements in computational speed and the emergence of graphics processing unit based technology [95,96] have reduced limitations of computational ability, opening the way for more complex models. This is already occurring in the form of 3D modeling, as seen in the ContraCancrum project described above, and even as hybrid PK-PD ABM with finite element solutions of the PDEs [97].…”

Section: Discussionmentioning

confidence: 99%

Integrated PK-PD and agent-based modeling in oncology

Wang¹,

Butner²,

Cristini

et al. 2015

J Pharmacokinet Pharmacodyn

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Mathematical modeling has become a valuable tool that strives to complement conventional biomedical research modalities in order to predict experimental outcome, generate new medical hypotheses, and optimize clinical therapies. Two specific approaches, pharmacokinetic-pharmacodynamic (PK-PD) modeling, and agent-based modeling (ABM), have been widely applied in cancer research. While they have made important contributions on their own (e.g., PK-PD in examining chemotherapy drug efficacy and resistance, and ABM in describing and predicting tumor growth and metastasis), only a few groups have started to combine both approaches together in an effort to gain more insights into the details of drug dynamics and the resulting impact on tumor growth. In this review, we focus our discussion on some of the most recent modeling studies building on a combined PK-PD and ABM approach that have generated experimentally testable hypotheses. Some future directions are also discussed.

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Graphics processing units accelerated semiclassical initial value representation molecular dynamics

Cited by 33 publications

References 92 publications

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

Integrated PK-PD and agent-based modeling in oncology

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