The power of VNA-driven quasi-optics to sense group molecular action in condensed phase systems

© © 20xx IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.The authors would like to thank the Engineering and Physical Sciences Research Council (EPSRC, UK) for generous support (EP/1014845)

Efficient model chemistries for peptides. II. Basis set convergence in the B3LYP method

Pre-print version of an article published as Phil. Nat. 1:1-18 (2009), Copyright Excogitation & Innovation Laboratory, the published version can be found at http://www.eilab.org/pn/v1i1/20090003.htmSmall peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to correctly describe the conformational behaviour of small peptides constitutes an unavoidable first step. In this work, we present an study of several potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The PESs are calculated using the B3LYP density-functional theory (DFT) method, with Dunning’s basis sets cc-pVDZ, aug-cc- pVDZ, cc-pVTZ, aug-cc-pVTZ, and cc-pVQZ. These calculations, whose cost amounts to approximately 10 years of computer time, allow us to study the basis set convergence of the B3LYP method for this model peptide. Also, we compare the B3LYP PESs to a previous computation at the MP2/6-311++G(2df,2pd) level, in order to assess their accuracy with respect to a higher level reference. All data sets have been analyzed according to a general framework which can be extended to other complex problems and which captures the nearness concept in the space of model chemistries (MCs).This work has been supported by the research projects DGA (Aragón Government, Spain) E24/3 and MEC (Spain) FIS2006-12781-C02-01. P. Echenique was supported by a MEC (Spain) postdoctoral contract

The power of VNA-driven quasi-optics to sense group molecular action in condensed phase systems

© 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.The versatility for quasi-optical circuits, driven by modern vector network analysers, is demonstrated for the purpose of low energy (meV) coherent spectroscopy. One such example is shown applied to the curing dynamics of a non-mercury-based dental cement. This highlights the special place the methodology holds as a `soft-probe' to reveal the time-resolved energetics of condensed phased systems as they self-organise to adopt their low energy state

Explicit factorization of external coordinates in constrained Statistical Mechanics models

If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, we explicitly write the determinant of the mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule, general internal coordinates and arbitrary constraints, as a product of two functions; one depending only on the external coordinates that describe the overall translation and rotation of the system, and the other only on the internal coordinates. This work extends previous results in the literature, proving with full generality that one may integrate out the external coordinates and perform Monte Carlo simulations in the internal conformational space of macromolecules. In addition, we give a general mathematical argument showing that the factorization is a consequence of the symmetries of the metric tensors involved. Finally, the determinant of the mass-metric tensor G is computed explicitly in a set of curvilinear coordinates specially well-suited for general branched molecules.Comment: 22 pages, 2 figures, LaTeX, AMSTeX. v2: Introduccion slightly extended. Version in arXiv is slightly larger than the published on

Simulations reveal the role of composition into the atomic-level flexibility of bioactive glass cements

K. V. T. thanks ETT-489/2009 and TAMOP-4.2.1.B, Hungary. D. D. T. thanks the UK's Royal Society for the award of a Royal Society Industry Fellowship. This research utilised Queen Mary's MidPlus computational facilities, supported by QMUL Research-IT and funded by EPSRC grant EP/K000128/1. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk)