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

Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada R. F. et al. (Ed.), Madrid: Aula Documental, 200

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)

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

Lithium Batteries and the Solid Electrolyte Interphase (SEI)—Progress and Outlook

Interfacial dynamics within chemical systems such as electron and ion transport processes have relevance in the rational optimization of electrochemical energy storage materials and devices. Evolving the understanding of fundamental electrochemistry at interfaces would also help in the understanding of relevant phenomena in biological, microbial, pharmaceutical, electronic, and photonic systems. In lithium-ion batteries, the electrochemical instability of the electrolyte and its ensuing reactive decomposition proceeds at the anode surface within the Helmholtz double layer resulting in a buildup of the reductive products, forming the solid electrolyte interphase (SEI). This review summarizes relevant aspects of the SEI including formation, composition, dynamic structure, and reaction mechanisms, focusing primarily on the graphite anode with insights into the lithium metal anode. Furthermore, the influence of the electrolyte and electrode materials on SEI structure and properties is discussed. An update is also presented on state-of-the-art approaches to quantitatively characterize the structure and changing properties of the SEI. Lastly, a framework evaluating the standing problems and future research directions including feasible computational, machine learning, and experimental approaches are outlined