Module also offered within study programmes:
General information:
Name:
Investigation of structures and dynamics of biomolecules with the use of large research facilities
Course of study:
2016/2017
Code:
JBF-3-003-s
Faculty of:
Physics and Applied Computer Science
Study level:
Third-cycle studies
Specialty:
-
Field of study:
Biophysics
Semester:
0
Profile of education:
Academic (A)
Lecture language:
Polish
Form and type of study:
Full-time studies
Course homepage:
 
Responsible teacher:
prof. dr hab. inż. Lankosz Marek (Marek.Lankosz@fis.agh.edu.pl)
Academic teachers:
prof. dr hab. inż. Lankosz Marek (Marek.Lankosz@fis.agh.edu.pl)
dr hab. inż. Bernasik Andrzej (bernasik@agh.edu.pl)
prof. dr hab. Burda Kvetoslava (kvetoslava.burda@fis.agh.edu.pl)
prof. dr hab. Kapusta Czesław (kapusta@agh.edu.pl)
dr hab. inż. Sikora Marcin (marcins@agh.edu.pl)
Module summary

Description of learning outcomes for module
MLO code Student after module completion has the knowledge/ knows how to/is able to Connections with FLO Method of learning outcomes verification (form of completion)
Social competence
M_K001 Student is understands the need for training and improving of competences BF3A_K01 Participation in a discussion
Skills
M_U001 Student is able to perform simple analyzes and simulations by oneself. Student is able to gain models of local atomic structure of selected materials. Student is able to prepare report on spectra analysis and modeling BF3A_U02, BF3A_U01 Execution of exercises,
Participation in a discussion,
Report,
Activity during classes
M_U002 Student is able to compare capabilities of various techniques applied in examination of biological samples. Student is able to perform analysis of absorption and emission spectra of x-ray BF3A_U02, BF3A_U01 Execution of exercises,
Participation in a discussion,
Report,
Activity during classes
Knowledge
M_W001 Student has knowledge in scope of high resolution X-ray spectroscopy, soft matter examination with the use of method based on photoelectron spectroscopy, secondary ions mass spectrometry and atomic force microscopy Student has knowledge in scope of physical principles of EXAFS spectroscopy, equppment and method of sample preparation BF3A_W01, BF3A_W02 Participation in a discussion,
Activity during classes
M_W002 Student has knowledge in the scope of synchrotron radiation nuclear nonelastic scattering and nuclear forward scattering application. Student has a knowledge in interaction of synchrotron radiation including ultra high intensities with matter BF3A_W01, BF3A_W02 Activity during classes,
Participation in a discussion
FLO matrix in relation to forms of classes
MLO code Student after module completion has the knowledge/ knows how to/is able to Form of classes
Lecture
Audit. classes
Lab. classes
Project classes
Conv. seminar
Seminar classes
Pract. classes
Zaj. terenowe
Zaj. warsztatowe
Others
E-learning
Social competence
M_K001 Student is understands the need for training and improving of competences - + + - - - - - - - -
Skills
M_U001 Student is able to perform simple analyzes and simulations by oneself. Student is able to gain models of local atomic structure of selected materials. Student is able to prepare report on spectra analysis and modeling - + + - - - - - - - -
M_U002 Student is able to compare capabilities of various techniques applied in examination of biological samples. Student is able to perform analysis of absorption and emission spectra of x-ray - + + - - - - - - - -
Knowledge
M_W001 Student has knowledge in scope of high resolution X-ray spectroscopy, soft matter examination with the use of method based on photoelectron spectroscopy, secondary ions mass spectrometry and atomic force microscopy Student has knowledge in scope of physical principles of EXAFS spectroscopy, equppment and method of sample preparation + - - - - - - - - - -
M_W002 Student has knowledge in the scope of synchrotron radiation nuclear nonelastic scattering and nuclear forward scattering application. Student has a knowledge in interaction of synchrotron radiation including ultra high intensities with matter + - - - - - - - - - -
Module content
Lectures:
  1. Application of high resolusion X-ray spectroscopy mehods (XES and RIXS) for examination of magnetic nanoparticles and organometallic compounds

    Physical principles of XES and RIXS methods, methodology of measurements and sample preparation for examinations will be presented. Most important results obtained with the use of these techniques recently will be discussed – 4 h

  2. Application of XPS, UPS, SIMS and AFM techniques in research on soft matter – 4h

    Lectures will comprise:
    -photoelectron spectroscopy in the range of soft X-ray (XPS) and (UPS)
    -secondary ions mass spectroscopy (SIMS)
    -atomic force microscopy (AFM) and related methods
    The lectures will concern analysis of elemental composition and chemical state od elements not only on surface of materials but also under surface layers with submicron thickness

  3. Applications of NIS (Nuclear Inelastic Scattering) and NFS (Nuclear Forward Scattering methods) for research on biological samples. -3h

    Discussed will be physical principles of methods based on Nuclear Inelastic Scattering and Nuclear Forward Scattering of synchrotron radiation. Presented will be examples of applications presented techniques for analysis of biological samples

  4. Applications of synchrotron radiation in biomedical research -2h

    The lecture will comprise application on synchrotrons and lasers on free electrons in biomedical research. Discussed will be following research techniques:
    -X-ray fluorescence microscopy
    -XANES techniques
    Examples of applications of above indicated methods for investigation of human origin tissues for medical diagnosis and pathological processes will be presented

  5. Applications of EXAFS method in biophysical research -2h

    In lecture physical principles of the method, equippment, sample preparation and representatively results of research will be discussed

Auditorium classes:
  1. Application of high resolusion X-ray spectroscopy mehods (XES and RIXS) for examination of magnetic nanoparticles and organometallic compounds Student will be acquainted with selected computational packages for analysis and modeling of spectra for high resolution x-ray spectroscopy and execution of simple analysis and modeling – 3h
  2. Applications of NIS (Nuclear Inelastic Scattering) and NFS (Nuclear Forward Scattering methods) for research on biological samples.-1h

    Discussion on the comparison between NIS as well as NFS techniques and similar measurement methods

  3. Applications of synchrotron radiation in biomedical research- 2h

    Applications of synchrotron radiation and X-ray free electron lasers in studies of tissues on single cells level will be discussed.
    The student will be acquainted with packages for processing of emission and absorption X-ray spectra

  4. Applications of EXAFS method in biophysical research -1h

    During the exercises, the participants will analyze EXAFS spectra for demonstration materials, and will simulate spectra with the use of specialist computer programs.
    Fitting the simulated spectra to experimental spectra, the models of local atomic structure of selected materials will be achieved

Laboratory classes:
  1. Application of high resolusion X-ray spectroscopy mehods (XES and RIXS) for examination of magnetic nanoparticles and organometallic compounds

    Student will be acquainted with selected computational packages for analysis and modeling of spectra for high resolution x-ray spectroscopy and execution of simple analysis and modeling-2h

  2. Application of XPS, UPS, SIMS and AFM techniques in research on soft matter:-3h

    Delivering of exemplary exercises

  3. Applications of synchrotron radiation in biomedical research -2h

    Conducting of calculations with the use of advanced computer packages for processing of X-ray absorption and emission spectra in studies of tissues

  4. Applications of EXAFS method in biophysical research – 1h

    During the exercises, the participants will analyze EXAFS spectra for demonstration materials, and will simulate spectra with the use of specialist computer programs.
    Fitting the simulated spectra to experimental spectra, the models of local atomic structure of selected materials will be achieved

Student workload (ECTS credits balance)
Student activity form Student workload
Summary student workload 45 h
Module ECTS credits 3 ECTS
Participation in lectures 15 h
Participation in auditorium classes 7 h
Participation in laboratory classes 8 h
Realization of independently performed tasks 15 h
Additional information
Method of calculating the final grade:

Lectures will be completed with credit without grade. The base of credit will be participation in discussion.
Auditorium classes will be credited (witout grade) on the base of participation in discussion
Laboratory classes will be credited (without grade) on the base of reports and participation in discussion.
The positive credits from all forms of classes will be base for credit of module

Prerequisites and additional requirements:

Prerequisites and additional requirements not specified

Recommended literature and teaching resources:

Will be announced by lecturers

Scientific publications of module course instructors related to the topic of the module:

Additional scientific publications not specified

Additional information:

None