讲座一: Postgraduate Study Opportunities in University College Dublin
演讲人：Prof.Nicolae-Viorel Buchete,
School of Physics, University College Dublin, Rm SCN 111, Dublin 4, Ireland
讲座时间：2017年6月6日上午10点
讲座地点：三教301室
摘要:
I will present a detailed overview of the Master programmes available at UCD with a focus on the 5 main MSC pathways that are available in the UCD School of Physics for the UCD-Nankai 1+1+1 program:
1.MSc Applied Mathematics and Theoretical Physics
2.MSc Computational Physics
3.MSc Nano-Bio Science
4.MSc Nano-Technology
5.MSc Space Science & Technology
I will also give an overview presentation of the general research areas available in our UCD School of Physics, and of the types of research projects that are available to postgraduate students.
讲座二：Coarse-Grained Kinetic Models of Protein Folding and Binding Networks
演讲人：Prof. Nicolae-Viorel Buchete,
School of Physics, University College Dublin, Rm SCN 111, Dublin 4, Ireland
讲座时间：2017年6月7日上午10点
讲座地点：三教301室
摘要:
I will first present a brief overview of the research areas available in our UCD School of Physics. Secondly, I will present the recent research in my own group at UCD in the area of theoretical and computational studies of protein folding and protein-protein interactions.
Protein folding and binding processes involve intrinsically complex mechanisms and corresponding pathways, which are notoriously difficult to study exhaustively, in a systematic manner. We show how master equations can be constructed and used to extract accurate coarse-grained kinetic models of the conformational dynamics of biomolecules, based on data from atomistic replica-exchange molecular dynamics simulations with explicit water molecules. By carefully controlling the effects of fast but often non-Markovian transitions, on one hand, and the typically limited sampling of slow relaxation processes on the other hand, we probe the underlying network of folding-unfolding and binding-unbinding transitions between the various configuration states of our biomolecular system. This systematic analysis reveals the important intrinsic conformational states and the associated transition pathways at multiple levels, from atomistic to coarse-grained representations. We validate our approach in several MD studies of amyloid-forming peptides, and of larger systems such as Cyclosporin A, and the helix-turn-helix subdomain of a viral scaffolding protein.
References:
[1] C.T. Leahy, R.D. Murphy, G. Hummer, E. Rosta, and N.V. Buchete, 'Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers', J. Phys. Chem. Lett. 7, 2676 (2016).
[2] Buchete N.V., and G. Hummer.; 'Coarse master equations for Peptide folding dynamics'. J. Phys. Chem. B, 112 (19):6057-6069 (2008).
[3] Sanchez-Sanz, G; Tywoniuk, B; Matallanas, D; Romano, D; Nguyen, LK; Kholodenko, BN; Rosta, E; Kolch, W; Buchete, NV, 'SARAH Domain-mediated MST2-RASSF Dimeric Interactions' PLoS Computational Biology, 12 (2016)
[4] Kelly, CM; Northey, T; Ryan. K; Brooks, BR; Kholkin, AL; Rodriguez, BJ; Buchete, NV; 'Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field'. Biophys. Chem., 196 :16-24 (2015).
[5] Kelly, CM; Muzard, J; Brooks, BR; Lee, GU; Buchete, NV 'Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules'. Physical Chemistry Chemical Physics, 17 :9634-9643 (2015)
Biography:
Nicolae-Viorel (Vio) Buchete is an Associate Professor of Theoretical & Computational Nano-Bio Physics in the UCD School of Physics. He has several postgraduate degrees from universities in both the USA (Boston University) and the EU (Al. I. Cuza University of Iasi, Romania, and University of Patras, Greece). He was awarded his PhD from Boston University, and he held research fellowships at the National Institutes of Health (Bethesda, MD, USA). His general research interests are in the areas of theoretical and computational biological physics, chemical physics, and nanoscience. Ongoing research projects in his group at UCD are concerned with statistical mechanics and molecular dynamics of biomolecular systems, systems biology, structural bioinformatics, and with multiscale modeling of biomolecules and complex fluids.
Prof. Buchete is the Head of Graduate studies in the UCD School of Physics, and the Director of the UCD MSc in Computational Physics Programme.
