Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

https://www.jstage.jst.go.jp/article/jjsth/26/1/26_17/_pdf

Seven-transmembrane receptors

We have known of azobenzene for over 150 years, the past 80 of which have seen the study and application of its photochromism. Azobenzene derivatives are now considered archetypical molecular switches, and their stability and reliability make them amenable to many fields of modern chemistry, materials science, biology and photopharmacology. When developing a photoswitch for a given application, a common approach is to tune the properties of an azobenzene. It is also possible to instead use heteroaryl azo dyes — motifs that are less popular even though their diversity offers distinct features. Despite the first discoveries of switching behaviour in heteroaryl azos and azobenzenes being coincident, the former have only recently begun to attract attention. This Review describes how the versatile and multifaceted characteristics of these scaffolds make them serious alternatives to azobenzene derivatives in molecular photoactuation. Heteroaryl azo photoswitches arguably deserve more consideration, and our survey of these systems includes challenges to their successful deployment. When presented with a light stimulus, heteroaryl azo photoswitches undergo molecular motion that can be harnessed for applications in materials science, catalyst design or drug development, among other fields. This Review describes selected subclasses of these versatile chemical motifs, covering their properties and prominent applications.

Heteroaryl azo dyes as molecular photoswitches

Molecular reaction dynamics

The recently developed method of frequency-, angle-, and time-resolved photoelectron imaging (FAT-PI) applied to the study of the dynamics of resonances of open-shell anions is reviewed The basic principles of the method and its experimental realisation are outlined The dynamics of a number of radical quinone anions is then considered Firstly, we show for para-benzoquinone how frequency- and angle-resolved photoelectron imaging provides finger-prints of the dynamics of resonances and then how time-resolved photoelectron imaging yields deep mechanistic insight into the relaxation dynamics of the resonances The effect of chemical substitutions of the para-quinone electrophore on the dynamics of resonances is discussed Increasing the conjugation leads to a greatly enhanced ability for resonances to decay to the ground electronic state of the radical anion Using time-resolved photoelectron spectroscopy, it is shown that the dynamics are facilitated by a bound valence state of the anion The addition of 

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Ultrafast dynamics of temporary anions probed through the prism of photodetachment

The resonant attachment of a free electron to a closed shell neutral molecule and the interplay between the following electron detachment and electronic relaxation channels represents a fundamental but common process throughout chemical and biochemical systems. The new methodology of anion frequency-resolved photoelectron imaging is detailed and used to map out molecular excited state dynamics of gas-phase para-benzoquinone, which is the electron accepting moiety in many biological electron-transfer chains. Three-dimensional spectra of excitation energy, electron kinetic energy, and electron ejection anisotropy reveal clear fingerprints of excited and intermediate state dynamics. The results show that many of the excited states are strongly coupled, providing a route to forming the ground state radical anion, despite the fact that the electron is formally unbound in the excited states. The relation of our method to electron impact attachment studies and the key advantages, including the extension to time-resolved dynamics and to larger molecular systems, are discussed.

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Anion Resonances of para-Benzoquinone Probed by Frequency-Resolved Photoelectron Imaging

A combined frequency-, angle-, and time-resolved photoelectron spectroscopy study is used to unravel the excited state dynamics following UV excitation of the isolated anionic chromophore of the green fluorescent protein (GFP). The optically bright S3 state, which is populated for hv > 3.7 eV, is shown to decay predominantly by internal conversion to the S2 state that in turn autodetaches to the neutral ground state. For hv > 4.1 eV, a new and favorable autodetachment channel from the S2 state becomes available, which leads to the formation of the neutral in an excited state. The results indicate that the UV excited state dynamics of the GFP chromophore involve a number of strongly coupled excited states.

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Excited state dynamics of the isolated green fluorescent protein chromophore anion following UV excitation.

The experimental determination of absolute total electron impact ionization cross-sections for polyatomic molecules has traditionally been a difficult task and restricted to a small range of specie...

Absolute Total Electron Impact Ionization Cross-Sections for Many-Atom Organic and Halocarbon Species

Isolated π-stacked dimer radical anions present the simplest model of an excess electron in a π-stacked environment. Here, frequency-, angle-, and time-resolved photoelectron imaging together with electronic structure calculations have been used to characterise the π-stacked coenzyme Q0 dimer radical anion and its exited state dynamics. In the ground electronic state, the excess electron is localised on one monomer with a planar para-quinone ring, which is solvated by the second monomer in which carbonyl groups are bent out of the para-quinone ring plane. Through the π-stacking interaction, the dimer anion exhibits a number of charge-transfer (intermolecular) valence-localised resonances situated in the detachment continuum that undergo efficient internal conversion to a cluster dipole-bound state (DBS) on a ∼60 fs timescale. In turn, the DBS undergoes vibration-mediated autodetachment on a 2.0 ± 0.2 ps timescale. Experimental vibrational structure and supporting calculations assign the intermolecular dynamics to be facilitated by vibrational wagging modes of the carbonyl groups on the non-planar monomer. At photon energies ∼0.6–1.0 eV above the detachment threshold, a competition between photoexcitation of an intermolecular resonance leading to the DBS, and photoexcitation of an intramolecular resonance leading to monomer-like dynamics further illustrates the π-stacking specific dynamics. Overall, this study provides the first direct observation of both internal conversion of resonances into a DBS, and characterisation of a vibration-mediated autodetachment in real-time.

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James N. Bull

Papers

Ultrafast dynamics of temporary anions probed through the prism of photodetachment

Anion Resonances of para-Benzoquinone Probed by Frequency-Resolved Photoelectron Imaging

Excited state dynamics of the isolated green fluorescent protein chromophore anion following UV excitation.

Absolute Total Electron Impact Ionization Cross-Sections for Many-Atom Organic and Halocarbon Species

Ultrafast dynamics of formation and autodetachment of a dipole-bound state in an open-shell π-stacked dimer anion