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Upcoming Thomas Young Centre events this July (No replies)
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Virtual tutorial on Theoretical Electrochemistry – Jun Cheng, XMA
Venue: online
Electrochemical interfaces are the place where matters and energy transform through electrochemical reactions, and by far the most important and difficult to study in a wide range of electrochemical applications including batteries and electrocatalysis. In the past two decades or so, ab initio methods have been extensively applied to model electrochemical interfaces. The first hurdle to overcome is how to compute and account for electrode potential in the simulations. I will discuss how it is treated using ab initio molecular dynamics (AIMD) and then extend to modeling of electric double layers, enabling us to elucidate the dynamic change of microscopic structures and capacitive response to applied potential. The high computational cost of AIMD however limits its application to small model systems consisting of hundreds of atoms at timescale of tens of ps. While, the latest development of AI accelerated AIMD (AI^2MD) significantly increases the size and timescale, showing great promise for in situ modeling of realistic electrochemical systems.
TYC Highlight Seminar: Enhanced sampling simulations in drug design – Alessio Lodola, University of Parma
Venue: online
Enhanced sampling methods are becoming increasingly important in modern computational medicinal chemistry, flanking standard approaches such as protein-ligand docking and molecular dynamics (MD). This is due to the impressive progresses made with GPU cards in terms of performance as well as with the development of improved codes. These progresses are making possible the exhaustive exploration of relevant degrees of freedom of protein-ligand complexes, with the possibility to simulate unbinding/binding events, accounting for conformational rearrangements and solvation effects. In these favorable conditions, the reconstruction of the free-energy surface (FES) of binding has become possible also on desk computers in less than a week of calculations, with an accuracy depending on the quality of the potential employed and on the approximations made in the definition of the virtual model under investigation. The FES of binding is of pivotal interest for rational drug design as its knowledge can allow to identify productive binding schemes for a small molecule to its target and to rank different ligands targeting the same receptor on a free-energy scale. In the present talk, I'll describe our recent experiences regarding the retrospective and perspective application of enhance sampling in drug design.
TYC Seminar: Understanding the action of pore forming proteins: Insights from molecular dynamics simulations, single molecule experiments and oligomerization kinetics – K Ganapathy Ayappa, Indian Institute of Science
Venue: Harrie Massey Lecture Theatre
The plasma membrane of our cells form the first line of defence to external threats. Protein-membrane interactions dominate this landscape, playing an important role in our understanding of a myriad of bacterial and viral infections. Phenomena range from membrane-assisted protein aggregation, oligomerization and folding. Pore-forming toxins a subclass of proteins expressed by bacteria form their primary arsenal responsible for over 30 % of bacterial infections. Pore forming proteins/toxins expressed in a water-soluble form bind to the target cellular membrane and self-assemble to form multimeric transmembrane pore complexes to eventually kill the cell. In this talk I will summarize our understanding of the pore forming toxin cytolysin A (ClyA) – a 34 kDa protein expressed by E. coli and known to undergo one of the largest conformational transitions during pore formation.
We use large scale molecular dynamics simulations at atomistic and coarse grained levels and enhanced free energy sampling methods in combination with experiments on supported bilayer and vesicle platforms to unravel the process of membrane insertion and kinetics of pore formation. Each of the different techniques offers unique insights at different length and time scales into membrane binding, influence of lipid composition as well as the inherent conformational changes that the protein undergoes during the pore formation process. We connect membrane insertion and ensuing conformational changes with recent superresolution and single molecule microscopy data to provide molecular insights into the pore forming pathway.
The Thomas Young Centre remains a renowned London-based interdisciplinary research network which brings together a range of groups across the capital whose research involves materials and molecular modelling and theoretical chemistry.