Charge Dependence of Temperature-Driven Phase Transitions of Molecular Nanoclusters: Molecular Dynamics Simulation

Phase transitions (liquid-solid, solid-solid) triggered by temperature changes are studied in free nanosized clusters of TeF_6 (SF_6) with different negative charges assigned to the fluorine atoms. Molecular dynamics simulations at constant energy show that the charge increase from q_F=0.1 e to q_F=0.25 e shifts the melting temperature towards higher values and some of the metastable solid states disappear. The increased repulsive interaction maintains the order in molecular systems at higher temperatures.Comment: 4 pages, 8 figures; presented at the conference on computational physics, Aachen (2001) accepted for publication in Comp.Phys.Com

Photoelectron imaging of the SO3 anion: vibrational resolution in photoelectron angular distributions*

The photoelectron imaging of the pyramidal sulphite radical monoanion is presented in the photon energy range spanning 3.10–4.45 eV. Two features are seen corresponding to formation of the ground electronic state of the neutral and to thermionic emission, which is seen for hv > 3.7 eV. Photoelectron spectra corresponding to direct detachment show vibrational structure associated with the v2 umbrella mode of the neutral. A similar structure is seen in the photoelectron angular distributions. The photoelectron angular distributions were modelled and agree with experiment. However, we cannot provide an explanation for the observed vibrational structure in the photoelectron angular distributions. The observed thermionic emission is assigned to the excitation to a pair of degenerate Feshbach resonances, which can internally convert and subsequently emit electrons statistically

Fingerprinting the Excited State Dynamics in Methyl Ester and Methyl Ether Anions of Deprotonated para-Coumaric Acid

Chromophores based on the para-hydroxycinnamate moiety are widespread in the natural world, including as the photoswitching unit in photoactive yellow protein and as a sunscreen in the leaves of plants. Here, photodetachment action spectroscopy combined with frequency- and angle-resolved photoelectron imaging is used to fingerprint the excited state dynamics over the first three bright action-absorption bands in the methyl ester anions (pCEs−) of deprotonated para-coumaric acid at a temperature of ≈300K. The excited states associated with the action- absorption bands are classified as resonances because they are situated in the detachment continuum and are open to autodetachment. The frequency-resolved photoelectron spectrum for pCEs− indicates that all photon energies over the S1(ππ∗) band lead to similar vibrational autodetachment dynamics. The S2(nπ∗) band is Herzberg-Teller active and has comparable brightness to the higher lying 21(ππ∗) band. The frequency-resolved photoelectron spectrum over the S2(nπ∗) band indicates more efficient internal conversion to the S1(ππ∗) state for photon energies resonant with the Franck-Condon modes (≈80 %) compared with the Herzberg-Teller modes (≈60%). The third action-absorption band, which corresponds to excitation of the 21(ππ∗) state, shows com- plex and photon-energy-dependent dynamics, with 20–40% of photoexcited population internally converting to the S1(ππ∗) state. There is also evidence for a mode-specific competition between prompt autodetachment and internal conversion on the red edge of the 21(ππ∗) band. There is no evidence for recovery of the ground elec- tronic state and statistical electron ejection (thermionic emission) following photoexcitation over any of the three action-absorption bands. Photoelectron spectra for the deprotonated methyl ether derivative (pCEt−) at photon energies over the S1(ππ∗) and S2(nπ∗) bands indicate diametrically opposed dynamics compared with pCEs−, namely intense thermionic emission due to efficient recovery of the ground electronic state

Ultrafast valence to non-valence excited state dynamics in a common anionic chromophore

Non-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S1(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S1(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold

Photoelectron spectroscopy of the deprotonated tryptophan anion: the contribution of deprotomers to its photodetachment channels †

Photoelectron spectroscopy and electronic structure calculations are used to investigate the electronic structure of the deprotonated anionic form of the aromatic amino acid tryptophan, and its chromophore, indole. The photoelectron spectra of tryptophan, recorded at different wavelengths across the UV, consist of two direct detachment channels and thermionic emission, whereas the hν = 4.66 eV spectrum of indole consists of two direct detachment features. Electronic structure calculations indicate that two deprotomers of tryptophan are present in the ion beam; deprotonation of the carboxylic acid group (Trp(i)−) or the N atom on the indole ring (Trp(ii)−). Strong similarities are observed between the direct detachment channels in the photoelectron spectra of tryptophan and indole, which in conjunction with electronic structure calculations, indicate that electron loss from Trp(ii)− dominates this portion of the spectra. However, there is some evidence that direct detachment of Trp(i)− is also observed. Thermionic emission is determined to predominantly arise from the decarboxylation of Trp(i)−, mediated by the ππ* excited state near λ = 300 nm, which results in an anionic fragment with a negative electron affinity that readily autodetaches

Temperature scaling in a dense vibro-fluidised granular material

The leading order "temperature" of a dense two dimensional granular material fluidised by external vibrations is determined. An asymptotic solution is obtained where the particles are considered to be elastic in the leading approximation. The velocity distribution is a Maxwell-Boltzmann distribution in the leading approximation. The density profile is determined by solving the momentum balance equation in the vertical direction, where the relation between the pressure and density is provided by the virial equation of state. The predictions of the present analysis show good agreement with simulation results at higher densities where theories for a dilute vibrated granular material, with the pressure-density relation provided by the ideal gas law, are in error. The theory also predicts the scaling relations of the total dissipation in the bed reported by McNamara and Luding (PRE v 58, p 813).Comment: ReVTeX (psfrag), 5 pages, 5 figures, Submitted to PR

Homogeneous cooling of rough, dissipative particles: Theory and simulations

We investigate freely cooling systems of rough spheres in two and three dimensions. Simulations using an event driven algorithm are compared with results of an approximate kinetic theory, based on the assumption of a generalized homogeneous cooling state. For short times $t$, translational and rotational energy are found to change linearly with $t$. For large times both energies decay like $t^{-2}$ with a ratio independent of time, but not corresponding to equipartition. Good agreement is found between theory and simulations, as long as no clustering instability is observed. System parameters, i.e. density, particle size, and particle mass can be absorbed in a rescaled time, so that the decay of translational and rotational energy is solely determined by normal restitution and surface roughness.Comment: 10 pages, 10 eps-figure

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin