|
Title
|
Matroid theory
|
||
|
Code
|
ÚMV/TMT/04
|
Teacher
|
Horňák Mirko
|
|
ECTS credits
|
5
|
Hrs/week
|
3/-
|
|
Assessment
|
Examination
|
Semester
|
3
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To acquaint
students with basic notions of matroid theory and possibilities of using
matroids in various disciplines of discrete mathematics.
|
||
|
Content
|
Independent
sets and bases. Properties of rank function. Closure operator. Circuits.
Duality in matroids. Hyperplanes. Submatroids. Restriction, contraction,
minor of a matroid. Transversals. Radó-Hall's Theorem and its
generalisations. Greedy algorithm versus matroids.
|
||
|
Recommended reading
|
D. J. A. Welsh, Matroid Theory, Academic Press,
1976
|
||
|
Title
|
Selected Topics in Probability
|
||
|
Code
|
ÚMV/VKP1/04
|
Teacher
|
Žežula Ivan
|
|
ECTS credits
|
5
|
Hrs/week
|
3/-
|
|
Assessment
|
Examination
|
Semester
|
3
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To present
the perspective of probability from the standpoint of measure theory and to
have students understand the most important results of probability theory.
|
||
|
Content
|
General
definition of probability. Distribution function and its properties. Basic
types of multivariate distributions. Conditional distributions and means.
Convolutions. Types of convergence of random variables. Strong law of large numbers.
Central limit theorems.
|
||
|
Alternate courses
|
ÚMV/VKP1/99
|
||
|
Recommended reading
|
Loeve: Probability theory, Van Nostrand, 1960
Rényi: Foundations of Probability, Holden-Day, 1970
|
||
|
Title
|
Differential and Integral Equations
|
||
|
Code
|
ÚMV/DIR/06
|
Teacher
|
Mihalíková Božena
|
|
ECTS credits
|
6
|
Hrs/week
|
3/1
|
|
Assessment
|
Examination
|
Semester
|
3
|
|
T/L method
|
Lecture, Practical
|
||
|
Content
|
Boundary
value problems. Asymptotic properties and the stability of linear
differential systems. Fredholm's integral equations with degenerate and
nondegenerate kernel. Integral equations with symmetric kernel.
|
||
|
Prerequisite courses
|
ÚMV/FAN/06 orÚMV/FAN/04
|
||
|
Recommended reading
|
P. Hartman, Ordinary differential equations, New
York, 1964
G.F.Trikomi, Integral equations, New York, 1967
|
||
|
Title
|
Combinatorial Optimisation
|
||
|
Code
|
ÚMV/KOO/04
|
Teacher
|
Jendroľ Stanislav, Lacko
Vladimír
|
|
ECTS credits
|
6
|
Hrs/week
|
3/1
|
|
Assessment
|
Examination
|
Semester
|
4
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
students basic knowledge about the
methods of modelling and controlling and how to apply them to typical
problems using methods of discrete mathematics.
|
||
|
Content
|
Complexity
of combinatorial algorithms. Sorting problems. Searching algorithms. Greedy algorithm. Trees and
spanning trees: rooted trees. Minimal spanning tree problem. Optimal path
problems. Introduction to network analysis. Distribution problems. Flows.
Assignment problem. The Chinese Postman problem. The Travelling Salesman
problem. Transportation problems.
|
||
|
Exclusive courses
|
ÚMV/KOA1/04
|
||
|
Recommended reading
|
N. Christofides: Graph Theory - An Algorithmic
approach, Academic Press, New York 1975 (ruský preklad z r. 1978).
J. Plesník: Grafové algoritmy, Veda Bratislava 1983.
G. Chartrand, O.R. Vellermann: Applied and
Algorithmic Graph Theory, McGraw-Hill, Inc. New York 1993.
|
||
|
Title
|
Functional Analysis
|
||
|
Code
|
ÚMV/FAN/06
|
Teacher
|
Doboš Jozef
|
|
ECTS credits
|
6
|
Hrs/week
|
3/1
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture, Practical
|
||
|
Content
|
Metric
spaces and their fundamental properties. Complete metric space and the
contrary mapping principle. Normed linear spaces. Hilbert's space. Linear
operators. The spectrum of the operator.
|
||
|
Recommended reading
|
N. Dunford, J.T. Schwartz, Linear operators, Part I,
Generaly theory, New York, 1963
N. Dunford, J.T. Schwartz, Linear operators, Part II,
Spectral theory, New York, 1963
|
||
Compulsory elective courses
|
Title
|
Mathematical Foundations of Cryptography
|
||
|
Code
|
ÚINF/MZK/06
|
Teacher
|
Geffert Viliam, Lacko
Vladimír
|
|
ECTS credits
|
6
|
Hrs/week
|
3/2
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture, Practical
|
||
|
Content
|
Classical
cryptography. Steganography. Conventional symmetric cryptography. Feistel
networks. Encryption modes: ECB, CBC, CFB, OFB. Security definitions. Models
of an adversary. Cryptoanalysis. Asymmetric cryptosystems. One-way functions
with trapdoors. RSA cryptosystem. El-Gamal cryptosystem. Generating large
prime numbers. Elliptic curves cryptography. Keyed Hash functions. Collision
resistant functions. Birthday paradox. SHA-1. Message authentication codes.
Password security. Digital signatures. Blind signatures. Key management.
X509. Certificates. Certification authorities. Electronic payments.
Electronic cash.
|
||
|
Exclusive courses
|
ÚINF/UKR1/03
|
||
|
Title
|
Real Functions Theory
|
||
|
Code
|
ÚMV/TRF/07
|
Teacher
|
Doboš Jozef
|
|
ECTS credits
|
5
|
Hrs/week
|
2/1
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture, Practical
|
||
|
Content
|
Continuity
properties of real functions, generalisations of continuity, quasi-uniform
convergence, sets of discontinuity points, stationary sets, determining sets,
metric preserving functions.
|
||
|
Title
|
Geometric Transformations
|
||
|
Code
|
ÚMV/GZ/04
|
Teacher
|
Ivančo Jaroslav
|
|
ECTS credits
|
5
|
Hrs/week
|
2/1
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To provide
deeper knowledge of projective spaces and transformation groups.
|
||
|
Content
|
Projective
spaces, Projective transformations, collineations. Fixed elements of a
collineation. A clasification of collineations.
|
||
|
Recommended reading
|
S. V. Duzhin, B. D. Chebotarevsky: Transformation
Groups for Beginers, AMS 2004
|
||
|
Title
|
Probability and Statistics
|
||
|
Code
|
ÚMV/PST1b/04
|
Teacher
|
Skřivánková Valéria, Ohriska Ján
|
|
ECTS credits
|
6
|
Hrs/week
|
2/2
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture, Practical
|
||
|
Content
|
Random
vectors, their distributions and characteristics. Correlation and regression.
Random sample, sampling distributions and characteristics. Point estimates
and their properties. Maximum likelihood method. Interval estimates;
confidence interval construction. Testing of statistical hypothesis; critical
region and level of significance. Parametric and nonparametric tests.
|
||
|
Recommended reading
|
Mandenhall W.: Introduction to probability and
statistics, PWS Publishers, Boston, 1987
Sincich T.: Statistics by example, Dellen Publishing
Company, New Jersey, 1990
|
||
|
Title
|
Game Theory
|
||
|
Code
|
ÚMV/TH1/04
|
Teacher
|
Cechlárová Katarína, Hajduková Jana
|
|
ECTS credits
|
6
|
Hrs/week
|
3/1
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
the basic methods of game theory and to have students model situations from
everyday life as simple games.
|
||
|
Content
|
Examples of
games. Extensive form of a game, value of the game. Von Neumann Morgenstern
theory of utility. Matrix games and their solution. Bimatrix games.Theory of
negotiations. n-person games: core, Shapley value. Economic applications of
game theory.
|
||
|
Alternate courses
|
ÚMV/TH1/99
|
||
|
Recommended reading
|
1. K. Binmore, Fun and games, D.C. Heath, 1992.
2. G.
Owen, Game Theory, Academic Press.
3. L.C. Thomas, Games, Theory and Applications, Wiley, New York.
4. H.S. Bierman, L.Fernandez, Game Theory with Economic
Applications, Addison-Wesley, 1998.
|
||
|
Title
|
Theory of Codes
|
||
|
Code
|
ÚMV/TKO1/04
|
Teacher
|
Horňák Mirko
|
|
ECTS credits
|
6
|
Hrs/week
|
4/-
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To acquaint
students with the basic principles and theoretical bases of text coding and
possibilities for their application.
|
||
|
Content
|
Monoids. Basic
notions of theory of codes. Examples of codes. Important classes of codes.
Maximal codes. Submonoids generated by codes. Stable submonoids. Group codes.
Free hull of a set of words. Test for recognising codes. Measure of a code.
Bernoulli distribution. Dyck code. Complete sets in monoids. Thin codes.
Composition of codes. Indecomposable codes.
|
||
|
Recommended reading
|
J. Berstel and D. Perrin, Theory of Codes, Academic
Press 1985
|
||
|
Title
|
Theory of Categories
|
||
|
Code
|
ÚMV/TK/07
|
Teacher
|
Ploščica Miroslav
|
|
ECTS credits
|
5
|
Hrs/week
|
2/1
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
students a categorical approach to various mathematical objects and
constructions. To provide basic knowledge about categories, functors and
natural transformations.
|
||
|
Content
|
Abstract
and concrete categories. Morphisms, monomorphisms, epimorphisms and
isomorphisms. Subobjects, quotient objects, free objects. Products and
copoducts. Limits and colimits, completeness.
Functors.
Natural transformations. Adjoint functors.
|
||
|
Recommended reading
|
Adámek J. : Theory of Mathematical Structures,
Reidel Publications, Dordrecht-Boston 1983
Mac Lane S., Birkhoff G.: Algebra, The
Macmillan Company, 1967
Lawvere F. W., Schanuel S. H.: Conceptual
Mathematics (A first introduction to categories), Cambridge University
Press 1997
Adámek J., Herrlich H., Strecker G.: Abstract and
concrete categories: The joy of cats, John Wiley and Sons, New York 1990
|
||
|
Title
|
Applied Linear Algebra
|
||
|
Code
|
ÚMV/ALA1/04
|
Teacher
|
Studenovská Danica
|
|
ECTS credits
|
5
|
Hrs/week
|
2/1
|
|
Assessment
|
Examination
|
Semester
|
2, 4
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
students basic knowledge about linear algebra; to make students able to apply
the theory in concrete excercises.
|
||
|
Content
|
Matrices
over Euclidean rings, canonical forms. Polynomial matrices. Similar matrices.
Jordan normal form. Functions of matrices, sequences, series. Inversion of
singular matrices, pseudoinverse matrices and their application.
|
||
|
Alternate courses
|
ÚMV/ALA1/99
|
||
|
Recommended reading
|
H.E.Rose: Linear algebra, A pure mathematical
approach, Birkhäuser Verlag, 2002
D.Serre: Matrices, Theory and applications, Springer
Verlag, 2002.
http://www.cs.ut.ee/~toomas_l/linalg/
|
||
|
Title
|
Fractal Geometry
|
||
|
Code
|
ÚMV/FRG1/03
|
Teacher
|
Bukovský Lev
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To
introduce students to the mathematical approach to analysing the concept of a
fractal with the possibility of using the results for the construction of
fractals.
|
||
|
Content
|
Concept of
a fractal. Basic topology of metric spaces. Self-similarity of a fractal.
Fractal as fixpoint of a mapping. Construction of a fractal by iteration.
Topological dimension and basic properties. Hausdorff measure and Hausdorff
dimension. Topological and Hausdorff dimension of particular fractals. Some
methods of construction of a fractal (topological dynamics).
|
||
|
Recommended reading
|
G. A. Edgar: Measure, Topology and Fractal Geometry,
Springer 1990.
K. Falconer, Fractal Geometry, John Willey 1992
H. O. Peitgen, H. Jurgens and D. Saupe, Fractals for
Classroom, I, II, Springer Verlag, Berlin 1991
|
||
|
Title
|
Number Theory
|
||
|
Code
|
ÚMV/TCI/04
|
Teacher
|
Harminc Matúš
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To
familiarise students with the divisibility and congruences of integers,
linear and quadratic congruences and arithmetic functions.
|
||
|
Content
|
Euclidean
algorithm. Fundamental theorem of arithmetic. Primes, composites, canonical
form and its applications. Congruences, criteria of divisibility. Arithmetic
functions. Euler’s theorem. Fermat’s theorem. Wilson’s theorem. Linear and
quadratic congruences.
|
||
|
Recommended reading
|
M. B. Nathanson: Elementary Methods in Number Theory.
Springer, 2000
H. E. Rose: A Course in Number Theory. Clarendon
Press, Oxford, 1994
|
||
Elective courses
|
Title
|
Foundations of Knowledge Systems
|
||
|
Code
|
ÚINF/ZNA1/06
|
Teacher
|
Vojtáš Peter
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
3
|
|
T/L method
|
Lecture
|
||
|
Content
|
Relations
of formal models: DBMS, SQL, and logic programming. Summary of different
formal models of computational processes, connections among them and
translations. Gentzenov systems, semantics and verification of programs.
Formal specifications, temporal logics: formulas, models, tableaux.
|
||
|
Recommended reading
|
M. Ben-Ari. Mathematical logic for Computer Science
2ed. Springer Verlag London 2001
J. Ullman. Principles of database and
knowledge based systems. Comp. Sci. Press 1988
J. W. Lloyd. Foundations of logic programming.
Springer Berlin 1987
|
||
|
Title
|
Theory of Information
|
||
|
Code
|
ÚMV/TIN1/03
|
Teacher
|
Bukovský Lev
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To
introduce students to mathematical attempts at solving selected problems of
computer science.
|
||
|
Content
|
Measurement
of information. Entropy and its properties. Shanon’s theorems. Coding and
basic types of codes. Using of algebraic structures in construction of codes.
Kolmogorov complexity. Basic properties and relation to the notion of
entropy. Complexity and randomness.
|
||
|
Recommended reading
|
J. H. van Lint, Introduction to Coding Theory,
Springer 1992
M. Li and P. Vitanyi, Kolmogorov Complexity and its
Applications, Handbook of Theoretical Computer Science, Elsevier, 1990, p.
188-252
|
||
|
Title
|
Control Theory
|
||
|
Code
|
ÚMV/TS1/04
|
Teacher
|
Cechlárová Katarína
|
|
ECTS credits
|
6
|
Hrs/week
|
3/1
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
students the basic concepts of controllable systems.
|
||
|
Content
|
Controllable
systems. Pontrjagin maximum principle. Linear systems, bang-bang
controls, singular controls.. Discrete
systems, dynamic programming, Bellmann’s optimality principle. Practical
applications of theoretical results.
|
||
|
Alternate courses
|
ÚMV/TS1/99 orÚMV/TS1/00
|
||
|
Recommended reading
|
K. Macki, A. Strauss: Introduction to Optimal Control
Theory, Springer, 1980
G. Feichtinger, R.F. Hartl: Optimale Kontrolle
okonomischer Prozesse, Berlin, 1986
|
||
|
Title
|
Computational Complexity
|
||
|
Code
|
ÚINF/VYZ1/04
|
Teacher
|
Geffert Viliam
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
1, 3
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To give
students background in the computational complexity and theory of
NP-completeness.
|
||
|
Content
|
Deterministic
and nondeterministic algorithms with polynomial time; NP-completeness.
Deterministic simulation of a nondeterministic Turing machine. Satisfiability
of Boolean formulae. Other NP-complete problems: satisfiability of a formula
in a conjunctive normal form, 3-satisfiability, 3-colorability of a graph,
3-colorability of a planar graph, knapsack problem, balancing, etc. Space
bounded computations, classes LOG-space and P-space. Deterministic
simulation: Savitch’s theorem. Closure under complement. Classification of
computational complexity of problems.
|
||
|
Alternate courses
|
ÚINF/VYZ1/03 orÚINF/VYZ1/00
|
||
|
Recommended reading
|
A.V.Aho and J.D.Ullman. The design and analysis of
computer algorithms. Addison-Wesley, 1974
P.van Emde Boas. Machine models and simulations. In
J.van Leeuwen (ed.): Handbook of theoretical computer science. North-Holland,
1990
Ch.K.Yap. Introduction to the theory of complexity
classes. To be published by Oxford Univ. Press. (Electronic version available
via anonymous ftp://cs.nyu.edu/pub/local/yap/complexity-bk).
|
||
|
Title
|
Algorithmically Unsolvable Problems
|
||
|
Code
|
ÚMV/ANP/03
|
Teacher
|
Bukovský Lev
|
|
ECTS credits
|
4
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To introduce
students to the most important results about the non-existence of an
algorithm for solving a given problem.
|
||
|
Content
|
Axiomatic
theories of natural numbers. Definability of recursive functions. Tarski’s
theorem on undefinability of truth in formalised arithmethic. Godel
incompleteness theorem. Algorithmic unsolvability of particular mathematical
problems. Non-existence of an algorithm for finding a solution to Diophantine
equations. Reduction of problems and degrees of unsolvability.
|
||
|
Recommended reading
|
J. Barwise ed., Handbook of Mathematical Logic, North
Holland 1977S. C. Kleene, Introduction to the Metamathematics, Van Nostrand
1952, ruský preklad Moskva 1957.
E. Mendelson, Introduction to Mathematical Logic, Van
Nostrand 1963.
M. Davis, Hilbert's Tenth Problem is Unsolvable,
Amer. Math. Monthly, 1973, 233--269.
|
||
PHYSICS
Study programme
Biophysics
(Full-time
master)
Code
Title ECTS Credit Hours/week
Assessment Recommended Year/Semester
Compulsory
courses
|
ÚFV/CHV1/03
|
Molecular Structure and Chemical Bonding
|
6
|
2/2
|
Examination
|
1/1
|
|
ÚFV/SP1/04
|
Semester Project
|
4
|
-/4
|
Assessment
|
1/1
|
|
ÚCHV/STA1/03
|
Structure Analysis
|
6
|
2/2
|
Examination
|
1/1
|
|
ÚFV/FCH1/02
|
Physical Chemistry for Biological Sciences
|
6
|
3/2
|
Examination
|
1/1
|
|
ÚCHV/BCH1a/03
|
Biochemistry I
|
3
|
2/-
|
Examination
|
1/1
|
|
KFaDF/DF2p/07
|
History of Philosophy
|
4
|
2/1
|
Examination
|
1/1
|
|
ÚFV/BME1/00
|
Introduction to Physics of Biological Membranes
|
3
|
2/-
|
Examination
|
1/2
|
|
ÚFV/EMB1b/04
|
Optical Spectroscopy
|
6
|
4/-
|
Examination
|
1/2
|
|
ÚCHV/BCH1b/03
|
Biochemistry II
|
5
|
3/-
|
Examination
|
1/2
|
|
ÚFV/EMB1d/04
|
Nuclear Magnetic Resonance
|
5
|
3/-
|
Examination
|
1/1
|
|
ÚFV/RP1/04
|
Annual Project
|
6
|
-/6
|
Assessment
|
1/2
|
|
ÚFV/SP2/04
|
Semester Project
|
6
|
-/6
|
Assessment
|
2/3
|
Compulsory
elective courses
|
ÚFV/NOT1a/03
|
Nontraditional Optimisation Techniques I
|
5
|
2/2
|
Examination
|
|
|
ÚFV/ZSY1/03
|
Complex Systems
|
5
|
2/2
|
Examination
|
|
|
ÚFV/MBB1/03
|
Fundamentals of Cellular and Molecular Biology
|
5
|
3/-
|
Examination
|
|
|
ÚFV/EMB1c/04
|
Modern Trends in Biophysical Methods
|
5
|
3/-
|
Examination
|
|
|
ÚFV/SBFc/03
|
Biophysical Seminar
|
1
|
-/1
|
Assessment
|
|
|
ÚFV/SBFe/03
|
Biophysical Seminar
|
1
|
-/1
|
Assessment
|
|
|
ÚCHV/ENZ/04
|
Enzymology
|
5
|
3/-
|
Examination
|
|
|
ÚFV/BSIM1/03
|
Biomolecular Simulations
|
6
|
2/2
|
Examination
|
|
|
ÚFV/BIOE1/02
|
Bioenergetics
|
3
|
2/-
|
Examination
|
|
|
ÚFV/PRb/04
|
Laboratory Training II: Optical Spectroscopy Methods
|
3
|
-/3
|
Assessment
|
|
|
ÚFV/PRd/04
|
Laboratory Training III: NMR
|
3
|
-/3
|
Zápočet
|
|
|
ÚFV/SBFd/03
|
Biophysical Seminar
|
1
|
-/1
|
Assessment
|
|
|
ÚFV/NOT1b/03
|
Nontraditional Optimisation Techniques II
|
5
|
2/2
|
Examination
|
|
|
ÚFV/NANO1/02
|
Nanotechnologies
|
3
|
2/-
|
Examination
|
|
|
ÚFV/MSA1/03
|
Methods of Structural Analysis
|
7
|
3/2
|
Examination
|
|
|
ÚFV/SBFf/03
|
Biophysical Seminar
|
1
|
-/1
|
Assessment
|
|
|
ÚFV/BMM1/05
|
Introduction to Physics of Biomacromolecules
|
3
|
2/-
|
Examination
|
|
|
ÚFV/ZBF1/05
|
Fundamentals of Biophotonics
|
3
|
2/-
|
Examination
|
|
Course units
Compulsory courses
|
Title
|
Molecular Structure and Chemical Bonding
|
||
|
Code
|
ÚFV/CHV1/03
|
Teacher
|
Uličný Jozef
|
|
ECTS credits
|
6
|
Hrs/week
|
2/2
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
actual methods used for computer simulations of molecules and to give
students hands-on experience with standard methods.
|
||
|
Content
|
Born-Oppenheimer
approximation. Methods and approaches of classical molecular mechanics. Force
fields and force constants for polyatomic simulations. Force fields for
biomolecular simulations (CHARMM, AMBER, MM2-4, MMFF, CVFF, etc.).
Independent electron approximation. Hartree-Fock self-consistent field
method. Post Hartee-Fock methods. Density functional theory (DFT): basic
principles and implementation. LSDA approximation and gradient corrected
methods. Hybrid methods. Wavefunction and electron density analysis. Limits
and perspectives of classical and quantum molecular mechanics. Alternative
methods. Ab initio computations and experimental observables.
Experimental and computational observables. Molecular dynamic and stochastic methods. Integration
algorithms. Car-Parinello dynamics.
|
||
|
Recommended reading
|
Leech: Molecular Modelling: Principles and
Applications, Longmann,
1996
M.P. Allen, D.J. Tildesley: Computer Simulation of
Liquids,
Oxford, University Press, 1989
P. W. Atkins, R. S. Friedman: Molecular Quantum
Mechanics.Oxford
University Press, 1997 (3. edition)
|
||
|
Title
|
Semester Project
|
||
|
Code
|
ÚFV/SP1/04
|
Teacher
|
Miškovský Pavol
|
|
ECTS credits
|
4
|
Hrs/week
|
-/4
|
|
Assessment
|
Assessment
|
Semester
|
1
|
|
T/L method
|
Practical
|
||
|
Objective
|
To realise
experimental and/or theoretical works within the frame of a chosen theme and
to present the results of this work in a consistent way.
|
||
|
Content
|
Work on a
chosen theme for the semester project in the Department of Biophysics.
|
||
|
Recommended reading
|
The literature will be recommended by supervisors of
individual works.
|
||
|
Title
|
Structure Analysis
|
||
|
Code
|
ÚCHV/STA1/03
|
Teacher
|
Černák Juraj
|
|
ECTS credits
|
6
|
Hrs/week
|
2/2
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To teach
students about symmetry at the micro- and macrostructural level, about diffraction methods used for crystal
structure determination and how to use the results of the crystal structure
analysis in their own work.
|
||
|
Content
|
Historical
introduction: importance of diffraction methods. Origin and properties of
x-rays. Elements of symmetry; space groups. Crystallographic systems; Bravais
unit cells. Miller indices. Theory of diffraction; Laue and Bragg equations.
Reciprocal space; Ewald construction. Single crystal diffraction methods;
automatic diffractometers. Powder diffraction: Debye-Scherrer and
diffractometric methods, their theory and use. Atomic factor, structure
factor, electronic density and their relationship. The phase problem:
overview of the methods for solving the phase problems. Refinement of the
structure; geometric parameters. Crystallisation processes; methods of
preparation of single crystals. Density. Basic inorganic structure types.
|
||
|
Recommended reading
|
Clegg W.: Crystal Structure Determination, Oxford
University Press, 1998
Luger, P.: Modern X-ray Analysis on Single Crystals.
Walter de Gruyter, Berlin, 1980
|
||
|
Title
|
Physical Chemistry for Biological Sciences
|
||
|
Code
|
ÚFV/FCH1/02
|
Teacher
|
Jancura Daniel, Miškovský Pavol
|
|
ECTS credits
|
6
|
Hrs/week
|
3/2
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture, Practical
|
||
|
Objective
|
To
introduce students to fundamental knowledge of physical chemistry emphasizing
the physico-chemical properties of biomacromolecules and biological systems.
|
||
|
Content
|
Description
of macroscopic systems, energy and 1st law of thermodynamics, entropy and 2nd
law of thermodynamics, Gibbs energy and equilibrium state, chemical
potential, binding constants of ligand-macromolecule interactions,
biophysical applications of the thermodynamics. Solutions, electrolytic
solutions, electrochemical equilibrium, electrodes, electrochemical
potential. Statistical thermodynamics: the interpretation of energy, heat,
entropy and information; the partition functions, biological applications of
statistical thermodynamics, the conformational transitions in proteins and
nucleic acids. Chemical reactions, chemical and biochemical kinetics,
dynamics of the chemical reactions, kinetics of enzymatic reactions,
inhibition of enzymes. Transport processes, molecular diffusion, membrane
transport and its significance for biological organisms.
|
||
|
Recommended reading
|
P. Atkins and J. de Paula: Physical chemistry (7th
Edition),
Oxford University Press, 2002
D. Eisenberg and D. Crothers: Physical chemistry with
applications to the life sciences,
Benjamin/Cummings, 1979
K. van Holde, W. Johnson and P. Ho, Principles of
physical biochemistry, Prentice Hall,
1988
|
||
|
Title
|
Biochemistry I
|
||
|
Code
|
ÚCHV/BCH1a/03
|
Teacher
|
Potočňák Ivan, Podhradský Dušan
|
|
ECTS credits
|
3
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
1
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To provide
understanding of life’s processes in molecular terms.
|
||
|
Content
|
Basic
structures of biomolecules. Structures and functions of saccharides and
lipids. Amino Acids and nucleic acids. Techniques of protein and nucleic acid
purification. Three-dimensional structures of proteins. Protein folding,
Dynamics and structural evolution. Hemoglobin: protein function in a
microcosm. Flow of genetic information. Proteosynthesis. Biosynthesis of
nucleic acids, replication, transcription and translation. Enzymes: structure
and function. Rates of enzymatic reactions Mechanisms of enzyme action and
control of enzymatic activity.
|
||
|
Recommended reading
|
Lubert Stryer and col.: Biochemistry 5th edition,
W.H.Freeman and Company, New York, 2003
Voet, Voet: Biochemistry 3rd edition, John Wiley
& sons, England, 2004
|
||
|
Title
|
Introduction to Physics of Biological Membranes
|
||
|
Code
|
ÚFV/BME1/00
|
Teacher
|
Fabriciová Gabriela, Miškovský Pavol
|
|
ECTS credits
|
3
|
Hrs/week
|
2/-
|
|
Assessment
|
Examination
|
Semester
|
2
|
|
T/L method
|
Lecture
|
||
|
Objective
|
To teach
the fundamental processes that occur in biological membranes.
|
||
|
Content
|
Structure
and models of membranes. Physico-chemical properties of biological membranes.
Functions of membranes. Propagation of nerve impulse and the process of
vision. Physical methods for the study of membranes.
|
||
|
Recommended reading
|
C.Hidalgo: Physical Properties of Biological
Membranes,Plenum Press, New York 1988
van Winkle I. J.: Biomembrane transport, Academic
Press, San Diego 1999
Stein W. D.: Channels, carriers, and pumps, Academic
Press, San Diego 1990
Glaser R.: Biophysics, Springer-Verlag, Heidelberg 1999
Pollard T. D., Earnshaw W. C.: Cell biology,
Saunders, Philadelphia 2004
Alberts: Molecular biology of the cell, Garland
Science, New York 2002
|
||
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