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Winter School 2018

PRACE Winter School 2018 - Timetable

Last Updated: Sunday, 02 September 2018

Winter School on Computational Chemistry, Biochemistry and Medicinal chemistry– Methods and Tools

November 26-29, 2018


Winter School on Computational Chemistry, Biochemistry and Medicinal chemistry– Methods and Tools

November 26-29, 2018


Day One, Mon 26/11

Mon 26/11


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.


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.


Coffee Break

  1. Dudev and C. Lim
  2. 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.


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.


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.



Day Two, Tue 27/11

Tue 27/11


Sonia Ilieva

Reaction mechanism in organic chemistry

10:00-10:30 Coffee Break

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. 


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.


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.


Coffee Break


Peicho Petkov,  Anela Ivanova

Optional Training



Day Three, Wed 28/11

Wed 28/11



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.


IvelinaGeorgieva, Natasha Trendafilova (IGIC-BAS)

Optional Training – Simulations of metal-organic complexes





Day Four, Thu 29/11

Thu 29/11


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.


Optional Training

IlianTodorov, Michael Seaton, Chin Yong, Alin Elena

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