Final project (EFN441L)

Final project

Innovation, IP protection, and application (VON101M)

This course will cover basics in intellectual property rights with emphasis on patents. What is intellectual property and when and how can they best be protected? How does intellectual property rights work (e.g. patents), and how can they be used and applied in innovation and industry. The system‘s organization will be covered, as well as the patent process, making a financial plan relating to patents, and database searches.

Quantum Mechanics 1 (EÐL509M)

The postulates and formalism of quantum mechanics. One-dimensional systems. Angular momentum, spin, two level systems. Particles in a central potential, the hydrogen atom. Approximation methods. Time independent and time dependent perturbation. Scattering.

Condensed Matter Physics 1 (EÐL520M)

The course is an introduction to some basic concepts of condensed matter physics. Curriculum: Chemical bonds, crystal structure, crystal symmetry, the reciprocal lattice. Vibrational modes of crystals, phonons, specific heat, thermal conductivity. The free electron model, band structure of condensed matter, effective mass. Metals, insulators and semiconductors. The course includes three labs.

Current topics in Chemistry and Biochemistry (EFN012F)

Lectures in contemporary research in chemistry and biochemistry:
Lectures in contemporary research in chemistry and biochemistry are given by invited speakers. Guest speakers will be from within the University of Iceland and from other universities, research institutes and companies.
Attendance is compulsory. Minimum of 8 lectures must be attended to complete the course.

Computational Chemistry F (EFN115F)

Methods for calculating and predicting properties of matter and the rate of transitions. Students will learn to use software for setting up and carrying out calculations of various organic and inorganic compounds and to interpret
the results for deeper insight and understanding of chemistry. Among the methods that will be introduced for calculating electron distribution are Hartree-Fock, density functional theory and perturbation theory (MP2). The compromises that need to be made in choosing basis sets and level of theory will be discussed.  Among methods used to calculate structure of molecules and movement of atoms are minimization techniques, classical dynamics, vibrational mode analysis, Monte Carlo and transition state theory.  The coursework includes laboratory exercises  involving computer calculations, including individual projects and computer programming.

Literature Study for the Master's Degree in Chemistry (EFN112F)

The supervising committee and the MS-student meet for one semester on a weekly basis to discuss research articles, review articles, and parts of books selected by the committee for that purpose. The reading material shall be related to the student's field of research, but without overlapping with it, so as to broaden the horizons of the student. The course is completed with a short thesis on the subject and an oral examination. The credits can be varied from 1 - 15 ECTS depending on the duration of the reading course. To be registered, students must contact the head of division of chemistry. 

Biochemistry 3 (LEF501M)

Practical class with accompanying lectures where practical and theoretical aspects of the experiments are discussed. Enzyme purification by hydrophobic, ion-exchange, affinity and gel filtration chromatography. Gel electrophoresis. Enzyme kinetics and inhibitors. Specific chemical modification of enzymes. Thermal stability of proteins. Ligand-protein interactions. Immunoprecipitation. Restriction enzymes and agarose electrophoresis.  Bioinformatics by computer.

Practical projects:
The following laboratory sessions are performed: Enzyme kinetics and the effect of inhibitors. Purification of enzymes by hydrophobic interactions, ion-exchange chromatography, affinity chromatography, and gel-filtration. Electrophoresis of protein and nucleic acids. Stability of proteins toward heating and urea/guanidinium assessed by activity measurements, UV-absorbance and circular dichroism. Determination of activation enery (Ea) and Gibb’s free energy. Specific reactions of amino acid side-chains in proteins for determining number of disulfide bonds and thiol groups. Action of reactive compounds as proteinase inhibitors differentiating between serine and cysteine proteases. Digestion of DNA by restriction enzymes and melting of DNA under various conditions that affect its stability. Preparation of samples for mass spectrometry by trypsin digestion and spotting of samples for MALDI-MS. Fingerprint identification using the computer program and database of Mascot. Bioinformatics and analysis of protein structures on the computer screen (e.q. BLAST, DeepView).

Applied Biochemistry (LEF509M)

Aimed at introducing students to aspects of applied biochemistry and biotechnology with emphasis on protein biotechnology. Lectures: Use of proteins in industry and medicine. Industrial use of enzymes. Enzyme reactors. Applications of immobilized enzymes. Biosensors. Use of recombinant DNA technology to genetically engineer organisms for production of biochemicals. Analytical biochemistry. Automaton in bioanalysis. Purification of bioproducts; scaling up of production lines and downstream processing. Tutorials: Recent research papers presented and discussed.

Teaching methods:
Lectures (about 40). Student lectures based on selected scientific papers.

The course is taught together with ILT102F - Introduction to Applied Biotechnology. Students can only take one of the courses, not both. 

Introduction to Pharmaceutical Sciences (LYF107M)

Pharmaceutical sciences is a versatile field that integrates diverse disciplines such as organic chemistry, biology and biochemistry to understand how we can develope new drugs that can improve current therapies or be first in line as a treatment. Thus, studies on their physicochemical properties, their formulation into suitable drug and their action inside the human body is needed. In this course we aim to provide the overview of this field in a comprehensive way. This course is aimed towards students with no background in pharmacy/pharmaceutical sciences.

Medicinal Chemistry/Drug Design (LYF302F)

The course will introduce different aspects of drug chemistry and drug development. Lectures: Drug receptors, activity assays, quantitative structure activity relationship (QSAR), computer assisted drug design, designing and defining compound libraries, ADMET properties and some drug development examples. A project will also be included in this course.

The project is to set up a Wikipeida page on subject matter linked to Drug Design.

Partial Differential Equations (STÆ505M)

The object of the course is to give a firm and rigorous foundation for more advanced studies in partial differential equations. Contents: first order equations; the Cauchy-Kowalevski theorem; techniques of analysis (Lebesgue-integral, convolutions, Fourier-transform); distributions; fundamental solutions; the Laplace operator; the heat operator.  The course is mainly intended for postgraduate students with a good background in analysis.

Thesis skills: project management, writing skills and presentation (VON001F)

Introduction to the scientific method. Ethics of science and within the university community.
The role of the student, advisors and external examiner. Effective and honest communications.
Conducting a literature review, using bibliographic databases and reference handling. Thesis structure, formulating research questions, writing and argumentation. How scientific writing differs from general purpose writing. Writing a MS study plan and proposal. Practical skills for presenting tables and figures, layout, fonts and colors. Presentation skills. Project management for a thesis, how to divide a large project into smaller tasks, setting a work plan and following a timeline. Life after graduate school and being employable.

Final project (EFN441L)

Episodes from the history of philosophy of science (SAG817M)

This course aims to introduce students to the nature and development of science by examining episodes of its history and by disucssing recent theories concerning the nature, aims, and development of science. A special emphasis will be placed on the history of physical science from Aristotle to Newton, including developments in astronomy during the scientific revolution of the 16th and 17th century. We will also specifically examine the history of Darwin’s theory of evolution by natural selection. These episodes and many others will be viewed through the lens of various theories of scientific progress, and through recent views about interactions between science and society at large. The course material may change depending on the students’ interest.

Modern Experimental Physics (EÐL616M)

Presentation of important techniques used in experimental physics and of various phenomena related to the subject matter of the second and third year of the Physics curriculum. Six extensive experiments are made, most of which are related to active research in experimental physics at the Science Institute of the University of Iceland.  The course emphasizes independence in carrying out the experiments, data analysis and literature search.

Life in the Universe (EÐL620M)

An introduction to astrobiology. Formation of the elements in the primordial plasma. Formation of heavy elements in stars and in their environments. Origin of galaxies, stellar systems, stars and planets. Formation of molecules and dust in the interstellar medium. Properties of Carbon and other elements necessary for life. Topics in biochemistry and thermodynamics. Origin and evolution of the Earth. Origin of water. The atmosphere. The Earth compared to other planets. What is life and what does it need? Origin and evolution of life on Earth. Life in extreme environments. Asteroids and impacts with the Earth. Effects of nearby supernovas. Is there life elsewhere in the Solar System, e.g. on Mars, Europa or Titan? Habitable worlds in the Universe. Extrasolar planets. The search for extraterrestrial intelligence. The Fermi paradox. Anthropic reasoning.

Introduction to Nanotechnology (EÐL624M)

Nanostructures and Nanomaterials, Nanoparticles, Nanowires, Thin films, thin film growth, growth modes, transport properties.  Characterization of nanomaterials, Crystallography,Particle Size Determination, Surface Structure, Scanning Tunneling Microscope, Atomic Force Microscope, X-ray diffraction (XRD), X-ray reflectometry (XRR), Scanning Electron Microscpe (SEM), and Transmission Electron Microscopy (TEM). Scaling of transistors, MOSFET, and finFET. Carbon Nanoscructures, Graphene and Carbon nanotubes. Lithography. Nanostructred Ferromagnetism. Nano-optics,  Plasmonics, metamaterials, cloaking and invinsibility. Molecular Electronics.

Molecular spectroscopy and reaction dynamics (EFN010F)

The course deals with the determination of the structure, energy levels, and reaction dynamics of molecules using the spectra resulting from the interaction between electromagnetic radiation and matter. The fundamentals of quantum mechanics applied to molecular spectra as well as experimental aspects of modern spectroscopic methods will be covered. The focus is on rotational and vibrational spectroscopies, electronic spectroscopy including time-resolved and single-molecule techniques, nuclear magnetic resonance, and electron paramagnetic resonance. The course involves weekly assignments and visits to experimental labs.

Current topics in Chemistry and Biochemistry (EFN011F)

Lectures in contemporary research in chemistry and biochemistry:
Lectures in contemporary research in chemistry and biochemistry are given by invited speakers. Guest speakers will be from within the University of Iceland and from other universities, research institutes and companies.
Attendance is compulsory. Minimum of 8 lectures must be attended to complete the course.

Literature Study for the Master's Degree in Chemistry (EFN214F)

The supervising committee and the MS-student meet for one semester on a weekly basis to discuss research articles, review articles, and parts of books selected by the committee for that purpose. The reading material shall be related to the student's field of research, but without overlapping with it, so as to broaden the horizons of the student. The course is completed with a short thesis on the subject and an oral examination. The credits can be varied from 1 - 15 ECTS depending on the duration of the reading course. To be registered, students must contact the head of division of chemistry. 

Organic Chemistry 4 (EFN608M)

The course is focused on modern methods to synthesise organic compounds with emphasis on systematic build-up of knowledge to deal with modern organic synthesis. This is added to knowledge based on previous courses in organic chemistry, Organic Chemistry 1, 2 and 3, being prerequisites to this course. The lectures will deal with various nucleophilic substitutions and electrophilic additions, modern organometallic chemistry, heterocycles, reduction and selective reducing agents, pericyclic reactions and the Woodward-Hoffmann rules, oxidations and rearrangements. Stereochemistry and stereocontrol will also be discussed and its importance in organic syntheses. Application of enzymes in organic sythesis will also be covered. Protective groups and their importance in organic sytnhesis will be discussed and systematic design and performance of organic synthesis such as umpolung, retrosynthesis, retrosynthetic analysis together with relevant concepts and theories. Finally, various classical organic synthesis of complicated natural products in historical perspectives will be described and discussed in details.

The course is intended for chemistry graduate students and students fulfillinng the prerequisites with the main aim to enable students to understand modern total synthesis of organic compounds.

Inorganic Chemistry 4 (EFN610M)

The aim of this course is to provide an overview of the diverse and fascinating discipline of advanced inorganic chemistry. The course is divided into three topics; 1) bioinorganic chemistry with emphasis on the reaction chemistry of metals in proteins; 2) Metal organic frameworks (MOFs): detailed description of the synthesis and structural analysis of MOFs and their functional properties such as gas adsorption and heterogeneous catalysis; 3) Chemistry and periodicity among metals and nonmetals. Inorganic cages, rings, and clusters. Inorganic polymers. Industrial production processes of metals and metalloids. Inorganic chemical industry in Iceland.
The focus is to provide students with the skills, knowledge and experience to develop their minds as professionals and independent researchers. This course will help students to understand and reason, how to approach a problem and evaluate their approaches by literature review followed by their analysis.
The minimum requirements for this course are Inorganic chemistry 1, 2 and 3. Although, the course is intended for graduate students in chemistry, it is open to others who fulfill the requirements. The main goals are to train students to read and analyse modern inorganic chemistry and chemical process in a meaningful and professional way.

Molecular spectroscopy and reaction dynamics (EFN612M)

The course deals with the determination of the structure, energy levels, and reaction dynamics of molecules using the spectra resulting from the interaction between electromagnetic radiation and matter. The fundamentals of quantum mechanics applied to molecular spectra as well as experimental aspects of modern spectroscopic methods will be covered. The focus is on rotational and vibrational spectroscopies, electronic spectroscopy including time-resolved and single-molecule techniques, nuclear magnetic resonance, and electron paramagnetic resonance. The course involves weekly assignments and visits to experimental labs.

Reaction Design (EVF602M)

This course provides an introduction to the design and analysis of chemical reactors, including batch, plug flow, continuous stirred tank reactors, and bioreactors. It covers key concepts in chemical thermodynamics, reaction kinetics, and catalysis, enabling students to develop a strong foundational knowledge in chemical reaction engineering. The course also includes guest lectures from industry experts and student presentations, fostering a connection to real-world applications.

Structure and Function of Proteins (LEF616M)

The characteristics of protein structures at the different structural levels. How structure determines the different properties of proteins. Structural classes of proteins and their characteristics. Relationship between molecular structure and biological function. Interactions that determine structural stability of proteins. Protein folding and unfolding. Effects of different parameters, e.g. temperature, pH, salts and denaturants on protein stability. Techniques used for determination structure and different properties proteins. Selected topics in protein structure function relationships.

Course plan: Lectures twice per week (2x40 min. each time). Computer lab once per week (2x40 min.). Lab sessions involve training using the WWW to study proteins. Tutorials and practice of using SwissPDBviewer program for solving specific assignments related to topics covered in lectures.

Biochemistry 4 (LEF617M)

This course focuses on methodology and recent innovations in biochemistry, emphasizing both analytical and computational techniques. It is divided into several modules, each taught by experts in their respective fields. While lectures form the core of the material, additional resources such as articles or book chapters may be assigned when appropriate. Practical demonstrations of research equipment may also be included. Students are expected to submit several written assignments throughout the semester.

The course will explore recent research in various specialized areas of biochemistry, and the content of the modules is regularly updated.

Topics covered may include single-molecule spectroscopy, protein mass spectrometry, structural biochemistry, binding affinity and thermodynamics, enzymology, and computational biochemistry.

Introduction to Systems Biology (LVF601M)

Systems biology is an interdisciplinary field that studies the biological phenomena that emerge from multiple interacting biological elements. Understanding how biological systems change across time is a particular focus of systems biology. In this course, we will prioritize aspects of systems biology relevant to human health and disease.

This course provides an introduction to 1) basic principles in modelling molecular networks, both gene regulatory and metabolic networks; 2) cellular phenomena that support homeostasis like tissue morphogenesis and microbiome resilience, and 3) analysis of molecular patterns found in genomics data at population scale relevant to human disease such as patient classification and biomarker discovery. In this manner, the course covers the three major scales in systems biology: molecules, cells and organisms.

The course activities include reading and interpreting scientific papers, implementation of computational algorithms, working on a research project and presentation of scientific results.

Lectures will comprise of both (1) presentations on foundational concepts and (2) hands-on sessions using Python as the programming language. The course will be taught in English.