Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the possibility of discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes

Automated Calculation of Thermal Rate Coefficients using Ring Polymer Molecular Dynamics and Machine-Learning Interatomic Potentials with Active Learning

We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials actively learning on-the-fly. Based on the original computational procedure implemented in the RPMDrate code, our methodology gradually and automatically constructs the potential energy surfaces (PESs) from scratch with the data set points being selected and accumulated during the RPMDrate simulation. Such an approach ensures that our final machine-learning model provides reliable description of the PES which avoids artifacts during exploration of the phase space by RPMD trajectories. We tested our methodology on two representative thermally activated chemical reactions studied recently by RPMDrate at temperatures within the interval of 300--1000~K. The corresponding PESs were generated by fitting to only a few thousands automatically generated structures (less than 5000) while the RPMD rate coefficients retained the deviation from the reference values within the typical convergence error of RPMDrate. In future, we plan to apply our methodology to chemical reactions which proceed via complex-formation thus providing a completely general tool for calculating RPMD thermal rate coefficients for any polyatomic gas phase chemical reaction

Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?

We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H2, D + MuH, and F + H2, and the prototypical polyatomic reaction H + CH4. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.TJHH acknowledges a Research Fellowship from Jesus College, Cambridge, and helpful comments on the manuscript from Stuart Althorpe. YVS acknowledges support via the Newton International Alumni Scheme from the Royal Society. YVS also thanks the European Regional Development Fund and the Republic of Cyprus for support through the Research Promotion Foundation (Project Cy-Tera ΝΕΑ ΓΠΟΔΟΜΗ/ΣΤΡΑΤΗ/0308/31).This is the author accepted manuscript. The final version is available from AIP via http://dx.doi.org/10.1063/1.492859

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes

Abstract Background: Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits

Thermal rate coefficients for the astrochemical process C + CH+ \u2192 C2++ H by ring polymer molecular dynamics

Thermal rate coefficients for the astrochemical reaction C + CH+\ue2\u86\u92 C2++ H were computed in the temperature range 20.300 K by using novel rate theory based on ring polymer molecular dynamics (RPMD) on a recently published bond-order based potential energy surface and compared with previous Langevin capture model (LCM) and quasi-classical trajectory (QCT) calculations. Results show that there is a significant discrepancy between the RPMD rate coefficients and the previous theoretical results that can lead to overestimation of the rate coefficients for the title reaction by several orders of magnitude at very low temperatures. We argue that this can be attributed to a very challenging energy profile along the reaction coordinate for the title reaction, not taken into account in extenso by either the LCM or QCT approximation. In the absence of any rigorous quantum mechanical or experimental results, the computed RPMD rate coefficients represent state-of-the-art estimates to be included in astrochemical databases and kinetic networks