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Saturday, April 9, 2011

Computability and Complexity

Preface 

Why do we need a formalization of the notion of algorithm or effective computation? In order to show that a specific problem is algorithmically solvable, it is sufficient to provide an algorithm that solves it in a sufficiently precise manner. However, in order to prove that a problem is in principle not solvable by an algorithm, a rigorous formalism is necessary that allows mathematical proofs. The need for such a formalism became apparent in the work of David Hilbert (1900) about the foundations of mathematics and Kurt Gödel (1931) about the incompleteness of elementary arithmetic.

The first investigations in the field were conducted by the logicians Alonzo Church, Stephen Kleene, Emil Post, and Alan Turing in the early 1930s. They provided the foundation of computability theory as a branch of theoretical computer science. The fundamental results established Turing computability as the correct formalization of the informal idea of effective calculation. The results led to Church’s thesis stating that ”everything computable is computable by a Turing machine”. The theory of computability has grown rapidly from its beginning. Its questions and methods are penetrating many other mathematical disciplines. Today, computability theory provides an important theoretical background for logicians and computer scientists.

Many mathematical problems are known to be undecidable such as the word problem for groups, the halting problem, and Hilbert’s tenth problem.

Contents - Computability:
  • Register Machine
  • Primitive Recursive Functions
  • Partial Recursive Functions
  • Ackermann's Function
  • Acceptable Programming Systems
  • Turing Machine
  • Undecidability
  • Word Problems

Thursday, April 7, 2011

Discrete Mathematics II - Lecture 1

The first lecture held on Wednesday covered the following topics:
  • basic definitions (graph, diagram, degree, degree sequence)
  • hand-shaking lemma
  • graph isomorphism
  • subgraphs
  • paths and cycles.

Discrete Mathematics II

The lecture takes place on Wednesday, 10:30 - 12:00 am, in building K - DE 15, room 0506, and will cover four topics:

  • graph theory
  • algorithmic graph theory
  • combinatorial optimization
  • linear optimization.

Thursday, February 24, 2011

Discrete Mathematics - Repetitorium

For more information, please check http://www.tu-harburg.de/ti6/aktuell.html

Tuesday, February 22, 2011

Seminar: DNA Computing

This seminar will not take place in the summer term 2011 due to other obligations.

Tuesday, February 8, 2011

Bioinformatics - Exam

1. Consider the following proteins from UniProtKB:

 P04655
 P04654
 P47710
 P08949
 P47851

a) Determine the families to which these proteins belong by using an appropriate tool.
Describe the consensus patterns of these families.

b) For each detected family, construct a multiple sequence alignment for the proteins belonging to the family. Find highly conserved regions in the proteins under consideration by examining the multiple sequence alignments. Are the consensus patterns of the families correctly reflected in the alignments?

c) Use a corresponding tool to provide a phylogenetic tree for the five proteins.
Does the tree reflect the family relationship correctly?

2. Consider the fibrinogen-binding protein from Staphylococcus aureus (accession P68799). Determine the secondary structure by a method of your choice.  Compare the predicted secondary structure for the given protein with the real one.

3. Basic Questions:
a) Explain the difference between standard Monte Carlo method and importance sampling.

b) How many genes has the HI virus?
 Which genes are not present in the human genome?

c) Given a phylogenetic tree with character data at the leaves:

            /\
           /  \
          /\  /\
        GCCA

Find the most parsimonious tree using Fitch's method.

d) What is an additive tree?

Friday, February 4, 2011

Discrete Mathematics - Lecture 14

Topics of the day:
  • Anwendung: Konstruktion endlicher Körper (siehe letzte Vorlesung).
  • Nullstellen und Einsetzungshomomorphismus.
  • Eulersche Phi-Funktion.
  • Satz von Euler und Kleiner Fermatscher Satz.
  • Potenzieren in Restklassenringen.
  • Anwendung: RSA-Algorithmus.