The aim of studying and bibliography

The main aim of study: Introducing the students to modern methods and computational tools used in biomolecular modeling. This knowledge is essential for studying of biotechnology processes (eg. conformation analysis, study of dynamic properties of biomolecules, designing new compounds, etc.).

The general information about the module: The module is implemented in the sixth semester. It includes 30 hours of lectures, 15 hours of laboratory and 30 hours of project. The module is ending with the credit.

Teaching materials: Instrukcje do ćwiczeń laboratoryjnych dostępne ze strony domowej koordynatora

Bibliography required to complete the module

Bibliography used during lectures

1	L. Piela	Idee chemii kwantowej	PWN, Warszawa.	2003
2	W. Kołos, J. Sadlej	Atom i cząsteczka	WNT Warszawa.	1998
3	A.D. Baxevanis, B.F.F. Quellette	Bioinformatyka. Podręcznik do analizy genów i białek	PWN, Warszawa.	2005
4	P. G. Higgs, T. K. Attwood	Bioinformatyka i ewolucja molekularna	PWN, Warszawa.	2008

Bibliography used during classes/laboratories/others

1

T.Pietryga

Instrukcje laboratoryjne

Katedra Chemii Fizycznej.

2012

Basic requirements in category knowledge/skills/social competences

Formal requirements: Registration for the given semester

Basic requirements in category knowledge: Basic knowledge in the physical chemistry, biochemistry and proteins

Basic requirements in category skills: Basic computer skills.

Basic requirements in category social competences: Ability of the cooperation and the work in the group

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	Has a basic knowledge of: -the methods of molecular and biomolecular modelling; -modeling of simple chemical reactions, spectroscopic spectra and ligand-receptor interactions; -prediction of secondary protein structure and space protein structure; -biomolecular data bases and homological analysis of protein; -structure-activity relatioships (QSAR).	lecture, laboratory	written test, written report	K_W03++ K_W14++	P6S_WG
02	Is able to apply basic methods of biomolecular modeling to study simple chemical reactions and to predict reactivity/activity of chemical compounds based on their structure and to estimate heat effects of simple chemical processes. Is able to model a simple biotechnological process using tools of biomolecular modeling.	laboratory, team project (2)	written raport, raport from the project	K_U08++ K_U19++ K_K03++	P6S_KR P6S_UO P6S_UW
03	Is able to find pieces of information in literature data bases and biomolecular data bases.	laboratory, team (2) project	written raport, raport from the project	K_U01++	P6S_UW
04	Is aware that biomolecular modeling process can be multivariant one and therefore is able to work alone and collectively, make decisions and follow instructions of superiors, responsible for the research. Is also aware of the fact that biomolecular modeling methods are constantly developing and understands the necessity of additional training and improving ones professional qualifications in this	lecture, laboratory, team (2) project	written test, written report	K_K01+ K_K03+	P6S_KK P6S_KR

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
6	TK01	Main conceptions of biomolecular modeling. Fundamentals of molecular modeling methods: molecular mechanics, molecular dynamics, Monte Carlo method. Molecular forces: covalent, electrostatic, hydrogen and hydrophobic interactions. Basics of molecular quantum mechanics: ab initio methods, semi-empirical methods, DFT method, hybrid methods. Methods of optimization of molecular geometry. Biotechnological bases, other biomolecular bases. Elements of homological analysis . Phylogenetic analysis in proteins. Protein modeling: amino acids, peptides, proteins – modeling of protein structure (primary, secondary, tertiary and quaternary structure). Application of molecular modeling methods in conformational analysis of biological systems. Study of reactivity by quantum chemistry methods. Computer modeling and study of reaction kinetics and thermodynamics. Application of molecular modeling methods in studies of active site reactivities of biochemical (enzymatic) systems, modeling of chemical reactions and transition states, spectroscopic spectra. Molecular docking: docking methods and algorithms, scoring functions of ligand-receptor interaction. Biomolecular modeling in the design of pharmacophores. Quantitative structure-activity relation QSAR methods (2D-QSAR, 3D-QSAR, 4D-QSAR, 5D-QSAR, 6D-QSAR). Kinds of structural indexes and techniques of their calculation. CoMFA and CoMSIA methods and their applications in biotechnology.	W30	MEK01
6	TK02	Data bases of structural proteins in biomolelular modelling. Homology and phylogenetic analysis of proteins. Minimization energy in peptides and proteins. Modeling of protein structure. Conformational analysis. Electrostatic properties of biomolecules. Examination of structure-activity relation (QSAR) Quantum chemistry investigation of antioxidative properties of flavonoids. Computer modeling of sun filters. Study of reactivity of enzyme systems, modeling of chemical reaction and its transition states. Molecular docking.	L15	MEK02 MEK03 MEK04
6	TK03	Carrying out of the assigned computational design.	P30	MEK02 MEK03 MEK04

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 6)		contact hours: 30.00 hours/sem.	complementing/reading through notes: 2.00 hours/sem. Studying the recommended bibliography: 15.00 hours/sem.
Laboratory (sem. 6)	The preparation for a Laboratory: 5.00 hours/sem.	contact hours: 15.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Project/Seminar (sem. 6)	The preparation for projects/seminars: 15.00 hours/sem.	contact hours: 30.00 hours/sem..	Doing the project/report/ Keeping records: 15.00 hours/sem.
Advice (sem. 6)		The participation in Advice: 3.00 hours/sem.
Credit (sem. 6)	The preparation for a Credit: 15.00 hours/sem.	The written credit: 1.00 hours/sem.

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture	Written credit of lecture covering the entire range of material of lecture. Evaluation of the test depends on the number of points scored: 3,0 (50,0 %-60,0%) MP ; 3,5 (60,1%-70,0%) MP; 4,0 (70,1%-80,0%) MP; 4,5 (80,1%-90,0%) MP; 5,0 (90,1%-100%) MP. MP- max. points.
Laboratory	Correct performance of laboratory exercises included in the schedule and correct preparation of written reports on every exercise.
Project/Seminar	Carrying out of a computational design, submission of written report on the project and its positive evaluation.
The final grade	Final grade (K): K = 0,50 w W + 0,50 w P; where: W, P - positive evaluation of the credit of lecture, project; w - factor related to the time of credit or project, w= 1.0 first term, w = 0.9 second term , w = 0.8 third term.The grade is rounded according to WKZJK.

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	K. Awsiuk; J. Bała; P. Chmielarz; E. Ciszkowicz; J. Raczkowska; M. Sroka; K. Wolski; I. Zaborniak	Grafting of Multifunctional Polymer Brushes from a Glass Surface: Surface-Initiated Atom Transfer Radical Polymerization as a Versatile Tool for Biomedical Materials Engineering	2024
2	K. Awsiuk; P. Chmielarz; M. Flejszar; N. Janiszewska; J. Raczkowska; K. Spilarewicz; K. Ślusarczyk; K. Wolski; M. Wytrwal	On the way to increase osseointegration potential: Sequential SI-ATRP as promising tool for PEEK-based implant nano-engineering	2024
3	K. Rydel-Ciszek	DFT Studies of the Activity and Reactivity of Limonene in Comparison with Selected Monoterpenes	2024
4	P. Błoniarz; P. Chmielarz; K. Kisiel; M. Klamut; K. Matyjaszewski; M. Niemiec; A. Pellis; C. Warne; I. Zaborniak	Controlled Polymer Synthesis Toward Green Chemistry: Deep Insights into Atom Transfer Radical Polymerization in Biobased Substitutes for Polar Aprotic Solvents	2024
5	G. Bartosz; P. Chmielarz; A. Dziedzic; N. Pieńkowska; I. Sadowska-Bartosz; I. Zaborniak	Nitroxide-containing amphiphilic polymers prepared by simplified electrochemically mediated ATRP as candidates for therapeutic antioxidants	2023
6	G. Bartosz; P. Chmielarz; M. Fahnestock; C. Mahadeo; N. Pieńkowska; I. Sadowska-Bartosz; I. Zaborniak	Induction of Oxidative Stress in SH-SY5Y Cells by Overexpression of hTau40 and Its Mitigation by Redox-Active Nanoparticles	2023
7	K. Awsiuk; P. Chmielarz; M. Flejszar; A. Hochół; J. Raczkowska; K. Spilarewicz; K. Ślusarczyk; K. Wolski; M. Wytrwal	Sequential SI-ATRP in μL-scale for surface nanoengineering: A new concept for designing polyelectrolyte nanolayers formed by complex architecture polymers	2023
8	P. Błoniarz; P. Chmielarz; M. Flejszar; A. Hochół; K. Spilarewicz; K. Ślusarczyk	Replacing organics with water: Macromolecular engineering of non-water miscible poly(meth)acrylates via interfacial and ion-pair catalysis SARA ATRP in miniemulsion	2023
9	P. Chmielarz; I. Zaborniak	How we can improve ARGET ATRP in an aqueous system: Honey as an unusual solution for polymerization of (meth)acrylates	2023
10	P. Chmielarz; I. Zaborniak	Polymer-modified regenerated cellulose membranes: following the atom transfer radical polymerization concepts consistent with the principles of green chemistry	2023
11	P. Chmielarz; M. Flejszar; A. Hochół	Advances and opportunities in synthesis of flame retardant polymers via reversible deactivation radical polymerization	2023
12	P. Chmielarz; M. Flejszar; K. Ślusarczyk	From non-conventional ideas to multifunctional solvents inspired by green chemistry: fancy or sustainable macromolecular chemistry?	2023
13	P. Chmielarz; M. Flejszar; M. Oszajca	Red is the new green: Dry wine-based miniemulsion as eco-friendly reaction medium for sustainable atom transfer radical polymerization	2023
14	P. Chmielarz; M. Flejszar; M. Sroka; M. Sroka; I. Zaborniak	Innowacyjne koncepcje syntezy polimerów technikami polimeryzacji rodnikowej z przeniesieniem	2023
15	P. Chmielarz; M. Korbecka; K. Matyjaszewski; Z. Michno; I. Zaborniak	Vegetable Oil as a Continuous Phase in Inverse Emulsions: ARGET ATRP for Synthesis of Water-Soluble Polymers	2023
16	P. Chmielarz; M. Sroka; I. Zaborniak	Modification of Polyurethanes by Atom Transfer Radical Polymerization and Their Application	2023
17	P. Chmielarz; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak	Bio-Inspired Iron Pentadentate Complexes as Dioxygen Activators in the Oxidation of Cyclohexene and Limonene	2023
18	M. Bockstaller; P. Chmielarz; T. Liu; K. Matyjaszewski; M. Sun; G. Szczepaniak; J. Tarnsangpradit; Y. Wang; Z. Wang; H. Wu; R. Yin; I. Zaborniak; Y. Zhao	Miniemulsion SI-ATRP by Interfacial and Ion-Pair Catalysis for the Synthesis of Nanoparticle Brushes	2022
19	P. Błoniarz; P. Chmielarz; K. Surmacz	Coffee Beverage: A New Strategy for the Synthesis of Polymethacrylates via ATRP	2022
20	P. Chmielarz; A. Górska; G. Grześ; K. Matyjaszewski; K. Pielichowska; Z. Wang; K. Wolski; I. Zaborniak	Maltotriose-based star polymers as self-healing materials	2022
21	P. Chmielarz; E. Ciszkowicz; K. Lecka-Szlachta; A. Macior; J. Smenda; K. Wolski; I. Zaborniak	A New Protocol for Ash Wood Modification: Synthesis of Hydrophobic and Antibacterial Brushes from the Wood Surface	2022
22	P. Chmielarz; H. Cölfen; M. Flejszar; M. Gießlb; J. Smenda; K. Wolski; S. Zapotoczny	A new opportunity for the preparation of PEEK-based bone implant materials: From SARA ATRP to photo-ATRP	2022
23	P. Chmielarz; I. Zaborniak	Comestible curcumin: From kitchen to polymer chemistry as a photocatalyst in metal-free ATRP of (meth)acrylates	2022
24	P. Chmielarz; I. Zaborniak	Nanofibers for the paper industry	2022
25	P. Chmielarz; M. Flejszar; A. Gennaro; A. Isse; M. Oszajca; K. Ślusarczyk; K. Wolski; M. Wytrwal-Sarna	Working electrode geometry effect: A new concept for fabrication of patterned polymer brushes via SI-seATRP at ambient conditions	2022
26	P. Chmielarz; M. Flejszar; M. Oszajca; J. Smenda; K. Ślusarczyk; K. Wolski; M. Wytrwal-Sarna	SI-ATRP on the lab bench: A facile recipe for oxygen-tolerant PDMAEMA brushes synthesis using microliter volumes of reagents	2022
27	P. Chmielarz; M. Sroka; I. Zaborniak	Lemonade as a rich source of antioxidants: Polymerization of 2-(dimethylamino)ethyl methacrylate in lemon extract	2022
28	K. Rydel-Ciszek	The most reactive iron and manganese complexes with N-pentadentate ligands for dioxygen activation—synthesis, characteristics, applications	2021
29	M. Caceres Najarro; P. Chmielarz; J. Iruthayaraj; A. Macior; I. Zaborniak	Lignin-based thermoresponsive macromolecules via vitamin-induced metal-free ATRP	2021
30	P. Chmielarz; A. Macior; I. Zaborniak	Smart, Naturally-Derived Macromolecules for Controlled Drug Release	2021
31	P. Chmielarz; A. Macior; J. Smenda; K. Wolski; I. Zaborniak	Hydrophobic modification of fir wood surface via low ppm ATRP strategy	2021
32	P. Chmielarz; A. Miłaczewska; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak	‘Oxygen-Consuming Complexes’–Catalytic Effects of Iron–Salen Complexes with Dioxygen	2021
33	P. Chmielarz; I. Zaborniak	Riboflavin-mediated radical polymerization – Outlook for eco-friendly synthesis of functional materials	2021
34	P. Chmielarz; M. Flejszar; J. Smenda; K. Wolski	Following principles of green chemistry: Low ppm photo-ATRP of DMAEMA in water/ethanol mixture	2021
35	P. Chmielarz; M. Flejszar; K. Ślusarczyk	Less is more: A review of μL-scale of SI-ATRP in polymer brushes synthesis	2021
36	P. Błoniarz; P. Chmielarz; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak; K. Surmacz; I. Zaborniak	Iron-Based Catalytically Active Complexes in Preparation of Functional Materials	2020
37	P. Chmielarz; A. Macior; I. Zaborniak	Stimuli-Responsive Rifampicin-Based Macromolecules	2020
38	P. Chmielarz; I. Zaborniak	Dually-functional riboflavin macromolecule as a supramolecular initiator and reducing agent in temporally-controlled low ppm ATRP	2020
39	P. Chmielarz; I. Zaborniak	Miniemulsion switchable electrolysis under constant current conditions	2020
40	P. Chmielarz; K. Matyjaszewski; I. Zaborniak	Synthesis of riboflavin-based macromolecules through low ppm ATRP in aqueous media	2020
41	P. Chmielarz; K. Surmacz	Low ppm atom transfer radical polymerization in (mini)emulsion systems	2020
42	P. Chmielarz; K. Surmacz; I. Zaborniak	Synthesis of sugar-based macromolecules via sono-ATRP in miniemulsion	2020
43	P. Chmielarz; K. Wolski; I. Zaborniak	Riboflavin-induced metal-free ATRP of (meth)acrylates	2020
44	P. Chmielarz; M. Flejszar	Surface modifications of poly(ether ether ketone) via polymerization methods – current status and future prospects	2020
45	P. Chmielarz; M. Flejszar; G. Grześ; K. Wolski; S. Zapotoczny	Polymer Brushes via Surface-Initiated Electrochemically Mediated ATRP: Role of a Sacrificial Initiator in Polymerization of Acrylates on Silicon Substrates	2020
46	P. Chmielarz; M. Flejszar; K. Surmacz; I. Zaborniak	Triple-functional riboflavin-based molecule for efficient atom transfer radical polymerization in miniemulsion media	2020
47	P. Chmielarz; M. Flejszar; R. Ostatek; K. Surmacz; I. Zaborniak	Preparation of hydrophobic tannins-inspired polymer materials via low ppm ATRP methods	2020
48	P. Chmielarz; M. Martinez; K. Matyjaszewski; Z. Wang; K. Wolski; I. Zaborniak	Synthesis of high molecular weight poly(n-butyl acrylate) macromolecules via seATRP: From polymer stars to molecular bottlebrushes	2020
49	P. Chmielarz; A. Gennaro; G. Grześ; A. Isse; A. Sobkowiak; K. Wolski; I. Zaborniak; S. Zapotoczny	Tannic acid-inspired star-like macromolecules via temporally-controlled multi-step potential electrolysis	2019
50	P. Chmielarz; I. Zaborniak	Temporally-controlled ultrasonication-mediated atom transfer radical polymerization in miniemulsion	2019
51	P. Chmielarz; I. Zaborniak	Ultrasound-mediated atom transfer radical polymerization (ATRP)	2019
52	P. Chmielarz; K. Matyjaszewski; I. Zaborniak	Modification of wood-based materials by atom transfer radical polymerization methods	2019
53	P. Chmielarz; M. Flejszar	Surface-initiated atom transfer radical polymerization for the preparation of well-defined organic-inorganic hybrid nanomaterials	2019