# Chemical Physics

## New submissions

[ total of 10 entries: 1-10 ]
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### New submissions for Tue, 20 Mar 18

[1]
Title: Mechanistic Regimes of Vibronic Transport in a Heterodimer and the Design Principle of Incoherent Vibronic Transport in Phycobiliproteins
Subjects: Chemical Physics (physics.chem-ph)

Following the observation of coherent oscillations in non-linear spectra of photosynthetic pigment protein complexes, particularly phycobilliprotein such as PC645, coherent vibronic transport has been suggested as a design principle for novel light harvesting materials operating at room temperature. Vibronic transport between energetically remote pigments is coherent when the presence of a resonant vibration supports transient delocalization between the pair of electronic excited states. Here, we establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that the role of coherent vibronic transport in pigment protein complexes should be reevaluated.

[2]
Title: Uncertainties in permittivities computed from molecular dynamics simulations and temperature correction of dielectric properties of condensed polar systems
Comments: 10 pages, 5 figures and 2 tables
Subjects: Chemical Physics (physics.chem-ph)

A robust, simple and fast procedure for the calculation of uncertainties in relative static dielectric permittivity ($\varepsilon_s$) computed via molecular dynamics (MD) is proposed. It arises as a direct application of well founded statistical methods for auto-correlated variables. Also, in order to deal with the lack of experimental data about $\varepsilon_s$ and relaxation times ($\tau$) at different temperatures, a method for their prediction is suggested. It requires one experimental value and at least two MD simulations. In the case of relaxation times, a theoretical justification is provided.

[3]
Title: Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation
Subjects: Chemical Physics (physics.chem-ph); Learning (cs.LG); Biological Physics (physics.bio-ph); Machine Learning (stat.ML)

As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the timescale of the latent space while inferring a reduced coordinate, which assists in finding slow processes as according to the variational approach to conformational dynamics. We additionally provide evidence that the VDE framework (Hern\'{a}ndez et al., 2017), which uses this autocorrelation loss along with a time-lagged reconstruction loss, obtains a variationally optimized latent coordinate in comparison with related loss functions. We thus recommend leveraging the autocorrelation of the latent space while training neural network models of biomolecular simulation data to better represent slow processes.

[4]
Title: Temperature dependent dynamics in water-ethanol liquid mixtures
Subjects: Chemical Physics (physics.chem-ph); Soft Condensed Matter (cond-mat.soft)

Temperature dependent hydrogen bond energetics and dynamical features, such as the diffusion coefficient and reorientational times, have been determined for ethanol-water mixtures with 10, 20 and 30 mol % of ethanol. Concerning pairwise interaction energies between molecules, it is found that water-water interactions become stronger, while ethanol-ethanol ones become significantly weaker in the mixtures than the corresponding values characteristic to the pure substances. Concerning the diffusion processes, for all concentrations the activation barrier of water and ethanol molecule become very similar to each other. Reorientation motions of water and ethanol become slower as ethanol concentration is increasing. Characteristic reorientational times of water in the mixtures are substantially longer than these values in the pure substance. On the other hand, this change for ethanol is only moderate. The reorientation motions of water (especially the ones related to the H-bonded interaction) become very similar for those of ethanol in the mixtures.

[5]
Title: Temperature dependent network stability in simple alcohols and pure water: the evolution of Laplace spectra
Subjects: Chemical Physics (physics.chem-ph)

A number of computer-generated models of water, methanol and ethanol are considered at room temperature and ambient pressure, and also as a function of temperature (for water and ethanol), and the potential model (for water only). The Laplace matrices are determined, and various characteristics of this, such as eigenvalues and eigenvectors, and the corresponding Laplace spectra are calculated. It is revealed how the width of the spectral gap in the Laplace matrix of H-bonded networks may be applied for characterising the stability of the network. A novel method for detecting the presence percolated network in these systems is also introduced.

[6]
Title: Ultrafast Photodynamics of Glucose
Journal-ref: J. Phys. Chem. B 2018, 122, 19-27
Subjects: Chemical Physics (physics.chem-ph)

We have investigated the photodynamics of $\beta$-D-glucose employing our field-induced surface hopping method (FISH), which allows us to simulate the coupled electron-nuclear dynamics, including explicitly nonadiabatic effects and light-induced excitation. Our results reveal that from the initially populated S$_{1}$ and S$_{2}$ states, glucose returns nonradiatively to the ground state within about 200 fs. This takes place mainly via conical intersections (CIs) whose geometries in most cases involve the elongation of a single O-H bond, while in some instances ring-opening due to dissociation of a C-O bond is observed. Experimentally, excitation to a distinct excited electronic state is improbable due to the presence of a dense manifold of states bearing similar oscillator strengths. Our FISH simulations explicitly including a UV laser pulse of 6.43 eV photon energy reveals that after initial excitation the population is almost equally spread over several close-lying electronic states. This is followed by a fast nonradiative decay on the time scale of 100-200 fs, with the final return to the ground state proceeding via the S$_{1}$ state through the same types of CIs as observed in the field-free simulations.

[7]
Title: Spectral analyses of trans- and cis-DOCO transients via comb spectroscopy
Comments: 4 figures, 3 tables
Subjects: Chemical Physics (physics.chem-ph); Optics (physics.optics)

We use time-resolved direct frequency comb spectroscopy in the mid-infrared to obtain high-resolution rovibrational spectra of products produced from the OD+CO reaction. In this work, we present spectral analyses for isotopologues of the transient DOCO radicals from this reaction in the OD stretch region. The analyses were performed with aid of two different theoretical approaches based on both perturbation theory and variational calculations used for prediction of rovibrational spectra of polyatomic molecules. We discuss the advantages and challenges of our current approach for studying spectroscopy and dynamics of transient molecules.

### Replacements for Tue, 20 Mar 18

[8]  arXiv:1706.09923 (replaced) [pdf, ps, other]
Title: A study of the dense Uniform Electron Gas with high orders of Coupled Cluster
Comments: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in "Neufeld, V.A. and Thom, A.J.W., J. Chem. Phys. 147, 194105 (2017)" and may be found at this https URL (following this https URL)
Journal-ref: J. Chem. Phys. 147, 194105 (2017)
Subjects: Chemical Physics (physics.chem-ph); Strongly Correlated Electrons (cond-mat.str-el)
[9]  arXiv:1801.08844 (replaced) [pdf, other]
Title: Identification of the fragment of the 1-methylpyrene cation by mid-IR spectroscopy
Comments: Chemical Physics Letters, Elsevier, In press
Subjects: Chemical Physics (physics.chem-ph)
[10]  arXiv:1803.05561 (replaced) [pdf, other]
Title: On the exact continuous mapping of fermions
Comments: 7-page manuscript (2 figures) with 11-page supplemental material
Subjects: Chemical Physics (physics.chem-ph); Statistical Mechanics (cond-mat.stat-mech); Quantum Physics (quant-ph)
[ total of 10 entries: 1-10 ]
[ showing up to 2000 entries per page: fewer | more ]

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