PRACE Winter School 2018 - Computational Chemistry, Biochemistry and Medicinal chemistry– Methods and Tools

26 Nov 2018, 08:00 → 29 Nov 2018, 18:00 Etc/GMT+2

National Centre for Supercomputing Applications, Bulgaria

This school aims to discuss the methodologies, numerical methods and their implementation used by the state-of-the-art codes in the HPC environment. The use of Computational (incl. HPC) methods and tools in the fields of Chemistry, Biochemistry and Materials science, areas in which the academics in Bulgaria have shown visible progress recognized globally will be demonstrated and exposed.

The attendants will learn the different techniques and their implementation in various codes, as well as will acquire the results that can be attained on the most recent HPC architectures. A particular focus will be the next technological developments and the possibilities that will be opened to chemists, biochemists and material scientists. Conditions for discussion and interaction with lecturers will be provided.

We shall bring the experiences of the UK’s Hartree Centre and the STFC Scientific Computing Department to show that knowledge exchange between scientists with different academic experience and between academia and industry is the facilitation process for setting collaborative projects in which academic and industrial interests, experiments, HPC modeling and application development meet to provide drive for one another.

A number of examples where the use of HPC modeling has been essential in solving scientific problems at atomic and molecular level will be present.

A basic introduction and training in some of the HPC applications developed at Daresbury Laboratory, relevant to collaborative projects of both academic and industrial nature it will also be provided.

The program is free of charge (not including travel and accommodation). For the hands-on sessions, participants are expected to bring their own laptops.

Applications are open to researchers, academics and industrial researchers residing in PRACE member countries, and European Union Member States and Associated Countries. All lectures and training sessions will be in English.

Information can be found also on the PRACE Winter School 2018 homepage.

notes http://scc.acad.bg/ncsa/index.php/en/levents/prace-winter-school-2018 The ICT-BAS building and its entrance

Monday, 26 November

09:30 → 10:00 Ilian Todorov: The Hartree Centre Experience

The presentation will outline the historical set up and current ambitions of the Hartree Centre at UKRI STFC, UK. The Hartree Centre together with IBM-UK provides a collaborative environment for commercial partners to set up and explore R&D project ideas in the computational area, including HPC Software Engineering, ML and AI. Its main function is to help advance and stimulate industrial innovation in the UK by applying academic methodologies and computational methods to industrially relevant problems.

10:00 → 11:00 Michael Seaton: UK Industrial Innovation via Hartree Centre’s Computational Soft Matter R&D

The talk will include a number of Hartree Centre research lines with commercial partners such as IBM and Unilever in the area of Soft Matter Computational Chemistry.

11:00 → 11:30 Coffee Break

11:30 → 13:00 T. Dudev and C. Lim S. Angelova, V. Nikolova, T. Spassov (FCP-SU, IOCCP-BAS)

(a) Factors governing the metal ion selectivity in ion channels: Insights from DFT/CDM calculations.

The thermodynamic aspects of metal ion competition in various ion channels (sodium, potassium, calcium and magnesium) have been systematically studied by a combination of density functional theory (DFT) calculations and continuum dielectric method (CDM) computations. The effect of different factors, such as the metal type, composition and architecture of the ion channel selectivity filter, solvent exposure of the pore and its rigidity, and the degree of the permeant ion hydration is assessed and major factors governing the metal ion selectivity in these systems determined.

(b) Determinants of the host–guest interactions between α-, β- and γ-cyclodextrins and group IA, IIA and IIIA metal cations: a DFT/PCM study

By employing density functional theory (DFT) calculations combined with polarizable continuum model (PCM) computations, we assess how the interaction between cyclodextrins of different size and a number of metal cations depends on (1) the size, valence state and preferred coordination number of the guest metal cations, (2) the size and flexibility of the host molecule, and (3) the dielectric properties of the environment. The major determinants of the process of cyclodextrin-metal recognition are established.

14:00 → 15:00 Anela Ivanova (FCP-SU): Biomolecular simulations for more efficient drug delivery

The workflow of a typical molecular dynamics (MD) simulation of bioactive components in the liquid phase is presented with focus on some specifics of biosimulations. An overview of the relevant MD algorithms is made, introducing their basics. Software packages are summarized, where these algorithms are implemented. The concepts are illustrated with sample results from recent atomistic MD simulations of different (supra)molecular building blocks of systems for efficient drug delivery of a model chemotherapeutic agent.

15:00 → 16:30 Ilza Pajeva (IBBE-BAS): In-silico methods in Drug design

The basics of in silico drug design will be given focusing on: concepts and principles of complementarity in the drug-receptor interactions, main types of ligand-receptor interactions, classifications of the methods in computer-aided drug design, examples and limitations.

Tuesday, 27 November

09:00 → 10:00 Sonia Ilieva: Reaction mechanism in organic chemistry

10:00 → 10:30 Coffee Break

10:30 → 12:00 Irini Doychinova (FP-MU Sofia): Case studies in drug design

Drug design is a rational computer-aided approach for drug discovery and development applying a wide variety of in silico methods. Some of the main methods like quantitative structure-activity relationships (QSARs), proteochemometrics, and molecular docking and their applications in drug design will be considered in the lecture by real case studies.

12:00 → 13:00 Boris Galabov: Computer modeling of π-hydrogen bonding in organic systems and grapheme

π-Hydrogen bonding is an important phenomena in chemistry, biology, physics, and material science. Computational modeling combined with FTIR spectroscopy reveals details of the interactions leading to the formation of π-hydrogen bonded complexes. Density functional theory and MP2 ab initio computations predict with a remarkable accuracy the shifts of O-H stretching vibration frequencies upon π-hydrogen bonding with benzene derivatives and graphene. It is shown that the O-H frequency shifts may be employed as an experimental measure of chemical reactivity for aromatic compounds.

14:00 → 15:00 Hristiyan A. Aleksandrov and Georgi N. Vayssilov: Modeling of metal and metal oxides systems relevant for catalytic applications

(a) Transformations of carbon and hydrocarbon species on transition metals – nanoparticle vs. slab models.
(b) DFT modeling of stability and vibrational frequencies of transition metal complexes
supported on zeolites and ceria.

15:00 → 15:30 Coffee Break

15:30 → 18:00 Peicho Petkov, Anela Ivanova: Optional Training

Wednesday, 28 November

09:00 → 13:00 Ilian Todorov: Introduction to DL_POLY and DL_MESO

DL_Software is the collective term that refers to the computational chemistry software suites developed at Daresbury Laboratory. DL_POLY is a general purpose molecular dynamics simulation package developed at Daresbury Laboratory by I.T. Todorov and W. Smith under the auspices of EPSRC and in support of CCP5. It can be used to simulate a wide variety of molecular systems including simple liquids, ionic liquids and solids, small polar and non-polar molecular systems, bio- and synthetic polymers, ionic polymers and glasses, solutions, simple metals and alloys. It is a widely used package in the UK and worldwide (see Molecular Simulation, 28 (2002), pp 385.

14:00 → 17:30 IvelinaGeorgieva, Natasha Trendafilova (IGIC-BAS): Optional Training – Simulations of metal-organic complexes

Thursday, 29 November

09:00 → 11:00 Chin Yong: Introduction to DL_FIELD

DL_FIELD is a computer program package written in C that primarily serves as a support application software tool for DL_POLY molecular dynamics simulation package. DL_FIELD is developed at Daresbury Laboratory by C.W. Yong under the auspices of EPSRC and in support of CCP5. The primary function of the Program is to convert users' atom models, in particular those of large complex bio molecular systems for a wide range of force fields (CHARMM, AMBER, OPLS, DREIDING, PCFF, CVFF, INORGANIC), into file formats that are recognisable by, and ready to run using, DL_POLY with minimum intervention by the user. The DL_FIELD operates with a minimum set of directive and, without having to learn any scripting languages, users can also easily fine tune force field models and set up their own force field library.

11:00 → 13:00 Michael Seaton: Introduction to DL_MESO

DL_MESO is a general purpose mesoscale simulation package developed at Daresbury Laboratory by M.A. Seaton under the auspices of EPSRC and in support of CCP5. It is written in Fortran90 and C++ and supports both Lattice Boltzmann Equation (LBE) and Dissipative Particle Dynamics (DPD) methods. It is supplied with its own Java-based Graphical User Interface (GUI) and is capable of both serial and parallel execution

14:30 → 17:30 IlianTodorov, Michael Seaton, Chin Yong, Alin Elena: Optional Training