Workshop On Molecular Modelling Of Materials And Biological Macromolecules

Workshop On Molecular Modelling Of Materials And Biological Macromolecules

The scenario of the industry has changed drastically over years and in the present times, the industrial skills demanded from students cannot be gained merely by academic courses. In such situations, various workshops play an imperative role in bridging this gap and enable the students to acquire industry-relevant skills.

NIT Rourkela has conducted different online workshops during the testing time of the Covid-19 pandemic to assist students to develop skills and expertise in interesting fields without any hindrance.

The 5-day workshop on Molecular Modelling of Materials and Biological Macromolecules was successfully conducted from Sept 22 – Sept 26, 2020, by the Department of Chemistry and Department of Metallurgy and Material Sciences, NIT Rourkela. The workshop aimed at equipping young researchers with essential knowledge of various molecular modelling techniques. Esteemed scientists and professors from some renowned science and engineering colleges across the country guided the students to boost their knowledge and skills.

Day 1

The workshop commenced with the inauguration ceremony. As the first keynote speaker, Prof. Saurav Pal was introduced. He currently serves as the director of IISER Kolkata, has been a former Professor IIT Bombay, President of the Federation of Asia chemical society and has guided over 30 PhD students and published 300 research papers.

Prof. Pal started his speech with general science matter, briefing about various opportunities in science from professional research to entrepreneurship. He also discussed the fact that major discoveries have been made out of either necessity, accident, or curiosity. This introduction was followed by mentioning the major challenges to scientific research in the COVID phase. The session speeded up as he introduced the notion of computational science and the transition from classical to quantum mechanics.

One of the most exciting topics of the speech was the Mixed Quantum theory. Moving forward to this, the density functional theory and catalyst designing were explained. The session ended up with a general talk about Hydrogen storage, LED’s, Nano-materials, and the Philosophy of Informatics.

Day 2 (First Session)

Professor T.K. Kundu was the speaker for this session. The session was titled “Density Functional Method for Material Modelling”. The talk started with the introduction of First Principle Methods. This included a sail through the Quantum Mechanics, from theories of Bohr, De Broglie, and Schrodinger to the first principle calculation using the Hartree Method.

The second topic addressed was the Density Functional Theory. The discussion started with mentioning the Hohenberg-Kohn theorems following which Kohn-Sham equations were introduced and participants were taught how to solve them. The speaker mentioned the Local Density Approximation and Generalized Gradient Approximation thereafter. In the middle of the session, the Discrete Fourier Transform was explained with some practical algorithms and its limitations. Towards the end of the speech, he explained the Electron localization Function and Adsorption/Desorption rate from the density of state calculations.

Day 2(second session)

Prof. Srabani Taraphder, Department of Chemistry, IIT Kharagpur was the speaker of this session. The session was titled a Computer simulation of an enzyme-catalyzed proton transfer reaction. She explained in detail about the activation energy in terms of potential energy hypersurface. Towards the end of the session, she talked about the empirical valence bond theory and the enzyme-catalyzed proton transfer reaction.

Day 3 (First session)

The speaker for the session was Dr Subhash Ganguly, Asst. Professor, Dept. of Metallurgy and Materials Engineering, NIT Raipur. Prof. Ganguly did his PhD from IIEST, Shibpur. His major areas of interest include Alloy Design, Computational Materials Science, Engineering Optimization, Genetic Algorithm, and Soft Computing. 

He guided students on handling problems related to alloy design using data science. In his talk, he emphasized the role of optimization in materials data science from an alloy design perspective. He briefed the students about how the scenario has transitioned from material driven technology culture to a technology-driven material research environment. As a result of this transition, demand for newer materials with complex properties has risen. Consequently, the research scenario is also changing. 

Data science is still in the embryo stage in the field of Metallurgy but it has a great scope shortly because it can be implemented in solving research-related challenges quickly. Prof. Ganguly imparted the knowledge of different stages of data science like descriptive analytics, diagnostic analytics, predictive analytics, and prescriptive analytics, and various optimization tools to the students. He also cited some research challenges as examples and guided the students on formulating their solutions implementing various techniques using data science.

Day 4 (First Session)

The speaker of the session was Prof. Jay Chakraborty. As Prof. Pal introduced him: MSC Physics, M.Tech from IITBHU (Gold Medalist), PhD from Max Planck Institute, currently a principal scientist at CSIR, National Metallurgical Labs. The topic of his speech was “Diffusion in Stressed Solids’’.

The whole talk was very elaborate and each slide had a plethora of different thermodynamic equations. He started with the basics of thermodynamics and later moved on to the basics of diffusion and chemical potentials for phase variable composition. The speaker uncovered various in-depth aspects very elegantly as he introduced Multicomponent and Substitutional diffusion followed by concepts of Diffusion in Hydrostatically stressed and Non-Hydrostatically stressed solids. The session ended with the derivation of the diffusion flux equation.

The next part of the session was to be delivered by Prof. Kaushik, who has done his MSC from Jadavpur University and PhD from IIT Kharagpur. Areas of his research interest mainly included Biological and Synthetic Biomolecules.

The first part of his speech dealt with the phenomena of Nucleosome Unwrapping in Single-Molecule Assays, where he started with the folding of DNA, nucleosome structure, and then the deeper aspects of the topic. Thereafter the topic was changed to “Shape Change of Polymersomes in presence of external stimuli”. The session ended with a tutorial guided by the professor.

Day 4(second shift)

The speaker of this session was Dr Sourab Sinha, a technical consultant, Scuba scientific software solutions Ltd. He talked about the Gaussian program and he talked in great detail about the expanding limits of computational chemistry and the transition state structures and the vibration in the molecule.

Day 5 (First session)

The speaker for the session was Dr Rajeev R, Asst. Professor, Dept. of Chemistry, NIT Rourkela. He did his PhD in Computational Chemistry from IIT Bombay. He pursued his postdoc from The Hebrew University of Jerusalem, Israel, and The Michigan Technological University, USA. The major areas of his interest are Computational Chemistry, Density Functional Theory (DFT), Metalloenzymes, Transition metal Catalysis, Stereoselectivity of enzyme catalysis.

His talk focussed on the modelling of bioinorganic complexes and metalloenzymes. He also emphasized the ways to circumvent the potential pitfalls related to it. He elaborately discussed the importance of QM/MM calculations, coherence between substrate binding specificity and correlated motions of proteins, enhancement of molecular orbital control by metalloenzymes, the role of heme and non-heme enzymes in HAT to overcome the steric barrier, aspects of efficient catalysis, and the importance of local electric field at the active site in controlling product selectivity.

The next part of the session covered the choice of theory and basic sets, size of QM & MM region, QM/MM partition, their coupling schemes, tips on the achievement of SCF convergence in QM/MM calculations. He also discussed Boltzmann corrected average barriers, deceptive barriers, spin density, and SNOs.

Day 5 (Second session)

The speaker for the session was Dr Ritwik Kavathekar, Application Scientist at Dassault Systems Ltd., Bengaluru. The major areas of his interest are Interphase Chemistry, Computational Material Science, Catalysts and excited states, Polymer Chemistry and DFT. He pursued MSc. in Chemistry from the University of Pune and a PhD in Computational Material Science from University College, Dublin.

He conducted a tutorial on molecular modelling using the Materials Studio Suite. He also talked about various other software that is useful at comprehensive research platforms like Electronic Lab Notebook (ELN), CISPro Chemical Inventory Management, Pipeline Pilot collection of libraries. He briefed the students about the functioning and history of Materials Studio and the CASTEP/ DMOL3 legacy. He also discussed materials modelling and multiscale modelling and guided the students on different methods employed in Materials Studio Suite. He illustrated examples ranging from simple molecules to the demanded complex product level calculations. 

The 5-days workshop indeed provided essential information on the basics of molecular modelling and advanced simulation techniques. These kinds of workshops have always been encouraged by our institute, and especially in these trying times, such organizations certainly help the students to grow through the pandemic.

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