The Cyprus Institute

About: The Cyprus Institute is a other organization based out in Nicosia, Cyprus. It is known for research contribution in the topics: Aerosol & Environmental science. The organization has 418 authors who have published 1252 publications receiving 32586 citations.

A ring polymer molecular dynamics study of the OH + H2(D2) reaction.

Abstract: In this work we have performed a ring polymer molecular dynamics (RPMD) study of the OH + H2 and OH + D2 reactions at temperatures ranging from 150 K to 2000 K using two available ab initio potential energy surfaces (PESs) that have been termed as the YZCL2 and NN1 PES, respectively. The YZCL2 PES was developed by Yang et al. [J. Chem. Phys., 2001, 115(1), 174] which is based on points fitted by a modified Shephard interpolation method and calculated with unrestricted coupled-cluster theory with all single and double excitations and a perturbative account of the triple excitations (UCCSD(T)) method with an aug-cc-pVQZ basis. The NN1 PES was constructed by Chen et al. [J. Chem. Phys., 2013, 138(15), 154301] using a neural networks method to fit ab initio energies calculated at the UCCSD(T)-F12a/AVTZ level of theory. We show that both techniques provide reliable PESs. The RPMD thermal rate coefficients and the kinetic isotope effects (KIEs) calculated using these two PESs are in very good agreement with each other as well as with previous experimental values available to date. Besides, we have shown that these two procedures for fitting PESs can yield even more similar RPMD rate coefficients when the same level of ab initio theory is employed, at least for the present OH + H2 reaction. Comparison of the previous theoretical calculations on the NN1 PES, namely, instanton theory and canonical variational theory with microcanonical optimized multidimensional tunneling, shows that the present RPMD results are more consistent and accurate. Future experimental measurements of the KIEs and accurate quantum mechanical calculations on these PESs are highly desirable, especially at low temperatures.

The new instrument using a TC–BC (total carbon–black carbon) method for the online measurement of carbonaceous aerosols

Abstract: . We present a newly developed total carbon analyzer (TCA08) and a method for online speciation of carbonaceous aerosol with a high time resolution. The total carbon content is determined by flash heating of a sample collected on a quartz-fiber filter with a time base between 20 min and 24 h. The limit of detection is approximately 0.3 µ g C, which corresponds to a concentration of 0.3 µ g C m −3 at a sample flow rate of 16.7 L min −1 and a 1 h sampling time base. The concentration of particulate equivalent organic carbon (OC) is determined by subtracting black carbon concentration, concurrently measured optically by an Aethalometer®, from the total carbon concentration measured by the TCA08. The combination of the TCA08 and Aethalometer (AE33) is an easy-to-deploy and low-maintenance continuous measurement technique for the high-time-resolution determination of equivalent organic and elemental carbon (EC) in different particulate matter size fractions, which avoids pyrolytic correction and the need for high-purity compressed gases. The performance of this online method relative to the standardized off-line thermo-optical OC–EC method and respective instruments was evaluated during a winter field campaign at an urban background location in Ljubljana, Slovenia. The organic-matter-to-organic-carbon ratio obtained from the comparison with an aerosol chemical speciation monitor (ACSM) was OM / OC = 1.8 , in the expected range.

Kinetics study of the CN + CH4 hydrogen abstraction reaction based on a new ab initio analytical full-dimensional potential energy surface

Abstract: We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300–1500 K, both theories agree within a factor of <2, reproducing the experimental behaviour taking into account the experimental uncertainties. At high temperatures, where the recrossing effects dominate and the RPMD theory is exact, both theories differ by a factor of about 20%; while at low temperatures this difference is larger, 45%. Note that in this temperature regime, the tunnelling effect is negligible. The CN + CH4/CD4 kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

Abstract: The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.