Next up in the Computational Chemistry seminars is Andy Ohlin who will talk about two topics: 1. Computational localised geochemistry and 2. ECCE.
When and where: 27 of June 2018 at 2 pm; location TBA.
Part 1. Geochemistry is more or less materials science focussing on naturally occurring matter. As such, computational geochemistry often focuses on molecular dynamics and/or planewave DFT, techniques which are suitable for periodic systems. Not us though. In line with our experimental work using discrete metal oxide clusters as models for extended surfaces we also do our computational work using localised basis set DFT. I’ll be talking about about how this approach can be used to explore geochemically relevant reactions by focussing on the issue of protonation in metal oxides.
Part 2. Computational chemistry typically has a steep learning curve, especially if the code you are using lacks a good GUI. Many years ago the Pacific Northwest National Lab set out to develop a GUI for their NWChem code, which they named ECCE. Due to a change in focus over the years PNNL support for ECCE waned until it finally got forked by me and a colleague at BYU. I’ll be introducing ECCE and will talk about the features that makes it so unique, and how it can be used for research — and education — in the department.
8/5 2018 – Rajendra Kumar gave a talk titled ‘The functional role of biomolecular elasticity – A molecular dynamics simulations perspective’.
Biomolecules go through large-scale motions to perform the biological functions. The motions with a underlying harmonic energy landscape are governed by their elastic properties. For example, bacteriophage Phi29 connector, a DNA channel protein and a component of viral DNA packaging motor, performs a large-scale twisting and stretching motions. The elastic properties of the Phi29 connector were characterized using the molecular dynamics (MD) simulations and its functional role were studied for the viral DNA packaging. The MD simulations revealed a quite heterogeneous distribution of stiff and soft regions, resembling that of typical composite materials that are also optimized to resist mechanical stress. In particular, the conserved middle α-helical region is found to be remarkably stiff, similar only to structural proteins forming viral shell, silk, or collagen. This rigid central region acts as a anchor point for flexible residues that strongly interact with the DNA and resists the DNA leakage against extreme internal pressure. Another most studied example for large-scale motions is the DNA bending, stretching and twisting motions that are governed by DNA elastic properties. Here, we propose an approach to quantify the elastic properties from MD simulations, particularly for DNA bending motions. This approach was validated by computing properties from microseconds MD simulations of 40 to 90 bp DNAs. Subsequently, this approach was employed on a bacterial TF Fis to study elasticities’ contribution to protein DNA binding specificity. Remarkably, the computed deformation free energy of bound DNA was linearly correlated with Fis-DNA binding affinity; therefore, the elasticities indeed contribute to the binding specificity. Our study suggests that elasticities should be considered to understand the protein DNA molecular recognition along with other known attributes.
The production of highly defective nanomaterials have opened an alternative approach to produce efficient catalysts. However, their complex elemental composition and crystal structure complicate their characterization and optimization as electrocatalysts, where not only a large density of active sites is desirable, but also an excellent electrical conductivity is required. Therefore, in this talk I will describe some computational methods used to facilitate the electrocatalyst design, in particular for the oxygen reduction reaction.
10/11 2017 – David Andersson gave a talk titled ‘Investigation of non-covalent interactions in Acetylcholinesterase-inhibitor complexes using density functional theory calculations‘.
22/9 2017 – Michael Holmboe gave a talk titled ‘Smectite clay systems studied with
Molecular dynamics simulations’
7/12 2016 Cecilia Lindgren/David Andersson gave a talk titled ‘Molecular dynamics simulations and immunology’.
20/10 2016 Thereza Soares gave a talk titled ‘Structural dynamics of biological membranes’?