Biophysics and Chemical Physics

Coordinated by: Institute of Physics Charles University
Study branch coordinator: prof. RNDr. Marek Procházka, Ph.D.

The focus of this field lies at the interface of physics, biology and chemistry. The study programme builds on a basic education in physics, deepening the focus on areas of theoretical and experimental physics important for the description and research of molecules, biopolymers, supramolecular systems and biological objects. The graduate will gain knowledge of quantum theory and the statistical physics of molecules and molecular systems, experimental methods of biophysics and chemical physics, especially optical and other spectroscopic methods, structural analysis and imaging techniques. Students choose one of two specializations: theoretical or experimental biophysics and chemical physics. In the theoretical specialization they will gain deeper knowledge in the field of quantum chemistry, molecular dynamics or advanced theoretical spectroscopy; in the experimental specialization, in the field of biochemistry and molecular biology, biophysics of photosynthesis or structural methods.

Profile of graduates and study aims:
The graduate knows quantum theory and the statistical physics of molecules and molecular systems, experimental methods of biophysics and chemical physics, especially optical and other spectroscopic methods, structural analysis and imaging techniques. Graduates of the theoretical specialization have deeper knowledge in the field of quantum chemistry, molecular dynamics or advanced theoretical spectroscopy. Graduates of the experimental specialization have deeper knowledge in the field of biochemistry and molecular biology, biophysics of photosynthesis or structural methods. Through regular seminars, master's theses, and thematically focused lectures, graduates have gained an idea of problems current in various fields and of methods of scientific work. They are proficient in communicating professional knowledge in the form of presentations and written texts, also in English. Some graduates can expect to pursue a career as a researcher. The acquired education also gives graduates employment opportunities in interdisciplinary teams dealing with physics, biology, chemistry, medicine, materials research, bio- and nano-technologies or pharmacy.

3.1 Recommended Course of Study

The field offers students two specializations - experimental and theoretical. Students usually select a specialization after the end of the first semester (first year of studies, winter semester). Until then, the courses of study in both specializations are the same.

Within each specialization, students have the opportunity to narrow the focus of their studies, which will be reflected in the choice of questions for the final state examination. Students choose two thematic areas (from three possible) and within these courses from the compulsory and optional courses of set I. In the experimental specialization, these include: 1. Biochemistry and molecular biology (courses NBCM012, NBCM008), 2. Optical spectroscopy and biophysics of photosynthesis (courses NBCM179, NBCM088) and 3. Structural methods (courses NBCM098, NBCM112). In the theoretical specialization, these include: 1. Quantum chemistry (courses NBCM121, NBCM122, NBCM155), 2. Molecular dynamics and statistics (courses NBCM346, NBCM100, NFPL004) and 3. Advanced theoretical spectroscopy (courses NBCM154, NBCM027, NOOE119).

Prerequisite for this study programme is a bachelor-level knowledge of quantum theory and general chemistry.

Specialization: Experimental biophysics and chemical physics

Compulsory and elective courses – set I (25 credits)

First year

CodeSubjectCreditsWinterSummer
NBCM010Bioorganic chemistry 42/1 C+Ex—
NBCM177Experimental methods of biophysics and chemical physics I 64/0 Ex—
NBCM160Classical and quantum statistical physics of molecular systems 43/0 Ex—
NBCM039Quantum Theory of Molecules 73/2 C+Ex—
NBCM095Practical Course in Experimental Methods of Biophysics and Chemical Physics I 70/5 MC—
NSZZ023Diploma Thesis I 6—0/4 C
NBCM178Experimental methods of biophysics and chemical physics II 3—2/0 Ex
NBCM088Biophysics of Photosynthesis 3—2/0 Ex
NBCM012Biochemistry 4—3/0 Ex
NBCM112Magnetic Resonance Methods in Biophysics 4—3/0 Ex
NBCM179Advanced methods of optical spectroscopy 4—3/0 Ex
NBCM103Practical Course in Experimental Methods of Biophysics and Chemical Physics II 7—0/5 MC

Second year

CodeSubjectCreditsWinterSummer
NSZZ024Diploma Thesis II 90/6 C—
NBCM175Seminar of biophysics and chemical physics I 30/2 C—
NSZZ025Diploma Thesis III 15—0/10 C
NBCM176Seminar of biophysics and chemical physics II 3—0/2 C
NBCM008Molecular and Cell Biology for Biophysicist 43/0 Ex—
NBCM098X-ray and Electron Structure Analysis of Biomolecules and Macromolecules 32/0 Ex—
NBCM165Theoretical bases of molecular spectroscopy 32/0 Ex—

Elective Courses – set II (15 credits)

CodeSubjectCreditsWinterSummer
NBCM101Detection and Spectroscopy of Single Molecules 32/0 Ex—
NBCM033Physical Principles of Photosynthesis 32/0 Ex—
NFPL185Advanced High Resolution NMR Spectroscopy 52/1 C+Ex—
NBCM158Practical aspects of experimental data treatment 31/1 Ex—
NBCM014Structure, Dynamics and Functions of Biomembranes 32/0 Ex—
NBCM023Importance and Functions of Metal Ions in Biological Systems 32/0 Ex—
NBCM102Fundamentals of Classical Radiometry and Photometry 32/0 Ex—
NBCM026Experimental Technology in Molecular Spectroscopy 3—2/0 Ex
NFPL179Quantum Description of NMR 5—2/1 C+Ex
NBCM114Optical Microscopy and Selected Imaging Techniques in Biophysics 3—2/0 Ex
NOOE012Scattering Methods in Optical Spectroscopy 3—2/0 Ex
NBCM097Surface-Enhanced Raman Spectroscopy 3—2/0 Ex
NBCM172Two-dimensional electronic spectroscopy 31/1 C+Ex1/1 C+Ex
NBCM316Computer Modelling of Biomolecules 41/2 C+Ex1/2 C+Ex
NBCM018One-week Practical Course in Biochemistry 30/2 C0/2 C

Recommended optional courses

CodeSubjectCreditsWinterSummer
NBCM121Ab Initio Methods and Density Functional Theory I 5—2/1 C+Ex
NBCM122Ab Initio Methods and Density Functional Theory II 32/1 C+Ex—
NBCM173Ab-initio methods for periodic systems 32/0 Ex—
NBCM307Astrobiology 32/1 Ex—
NBCM024Yeast Biology 3—2/0 Ex
NBCM150Physical observation of nano-objects 52/1 C+Ex2/1 C+Ex
NAFY018Chemistry for Physicists 42/1 C+Ex—
NBCM106Chemistry for Physicists II — Analytical Chemistry 6—2/2 C+Ex
NBCM156Chiroptic spectroscopy 3—2/0 Ex
NBCM154Quantum electrodynamics 3—2/0 Ex
NBCM134Quantum Theory of Resonances 3—2/0 Ex
NBCM051Molecular Dynamics and Monte Carlo Methods 52/1 C+Ex—
NBCM346Molecular dynamics I 5—2/1 C+Ex
NBCM347Molecular dynamics II 52/1 C+Ex—
NBCM181Molecular dynamics — calculations of free energy 31/2 MC1/2 MC
NBCM055Molecular Simulations for solving of material structure 52/1 C+Ex2/1 C+Ex
NBCM149Nanotechnology in biology 32/0 C2/0 C
NOOE119Nonlinear Optical Spectroscopy 3—2/0 Ex
NFPL004Nonequilibrium Statistical Physics and Thermodynamics 32/0 Ex—
NBCM305Optical Sensors 32/0 Ex—
NBCM099Practical Exercises in Quantum Theory of Molecules I 4—0/3 C
NBCM116Practical Exercises in Quantum Theory of Molecules II 40/3 C—
NAFY080Preparation of Biological Samples 3—2/0 Ex
NOOE015Seminar 2—0/1 C
NFPL186Seminar on High Resolution NMR Spectroscopy 30/2 C0/2 C
NBCM027Symmetry of Molecules 4—2/1 C+Ex
NFPL003Synthetic Problems of Quantum Theory 3—2/0 C
NBCM115Scientific Photography and Related Imaging Techniques 31/1 Ex—
NPRF005UNIX and LINUX for Physicists 32/0 C—
NBCM159Introduction to Computer Control of Experiment 4—1/2 MC
NBCM308Introduction to Protein Structure Studies 3—2/0 Ex
NBCM100Computational Experiments in Molecular Theory I 4—0/3 MC
NBCM125Computational Experiments in Molecular Theory II 6—0/4 MC
NBCM041Fundamentals of Energy Transfer in Molecular Systems I 32/0 Ex—

Specialization: Theoretical biophysics and chemical physics

Compulsory and elective courses – set I (25 credits)

First year

CodeSubjectCreditsWinterSummer
NBCM010Bioorganic chemistry 42/1 C+Ex—
NBCM177Experimental methods of biophysics and chemical physics I 64/0 Ex—
NBCM160Classical and quantum statistical physics of molecular systems 43/0 Ex—
NBCM039Quantum Theory of Molecules 73/2 C+Ex—
NBCM095Practical Course in Experimental Methods of Biophysics and Chemical Physics I 70/5 MC—
NSZZ023Diploma Thesis I 6—0/4 C
NBCM178Experimental methods of biophysics and chemical physics II 3—2/0 Ex
NBCM121Ab Initio Methods and Density Functional Theory I 5—2/1 C+Ex
NBCM154Quantum electrodynamics 3—2/0 Ex
NBCM346Molecular dynamics I 5—2/1 C+Ex
NBCM100Computational Experiments in Molecular Theory I 4—0/3 MC

Second year

CodeSubjectCreditsWinterSummer
NSZZ024Diploma Thesis II 90/6 C—
NBCM175Seminar of biophysics and chemical physics I 30/2 C—
NSZZ025Diploma Thesis III 15—0/10 C
NBCM176Seminar of biophysics and chemical physics II 3—0/2 C
NBCM122Ab Initio Methods and Density Functional Theory II 32/1 C+Ex—
NBCM155Field theory methods in the theory of many particles 32/0 Ex—
NFPL004Nonequilibrium Statistical Physics and Thermodynamics 32/0 Ex—
NBCM027Symmetry of Molecules 4—2/1 C+Ex
NBCM165Theoretical bases of molecular spectroscopy 32/0 Ex—
NOOE119Nonlinear Optical Spectroscopy 3—2/0 Ex

Elective Courses – set II (15 credits)

CodeSubjectCreditsWinterSummer
NBCM067Quantum Optics I 52/1 C+Ex—
NBCM347Molecular dynamics II 52/1 C+Ex—
NBCM131Advanced Methods in Molecular Dynamics 32/0 Ex—
NBCM041Fundamentals of Energy Transfer in Molecular Systems I 32/0 Ex—
NBCM093Quantum Optics II 5—2/1 C+Ex
NBCM134Quantum Theory of Resonances 3—2/0 Ex
NBCM099Practical Exercises in Quantum Theory of Molecules I 4—0/3 C
NBCM116Practical Exercises in Quantum Theory of Molecules II 40/3 C—
NBCM125Computational Experiments in Molecular Theory II 6—0/4 MC
NBCM055Molecular Simulations for solving of material structure 52/1 C+Ex2/1 C+Ex
NBCM180Theoretical seminar of biophysics and chemical physics 20/1 C0/1 C

Recommended optional courses

CodeSubjectCreditsWinterSummer
NBCM173Ab-initio methods for periodic systems 32/0 Ex—
NBCM307Astrobiology 32/1 Ex—
NBCM184Asymptotic Methods in Physics 52/1 C+Ex—
NBCM088Biophysics of Photosynthesis 3—2/0 Ex
NBCM012Biochemistry 4—3/0 Ex
NBCM101Detection and Spectroscopy of Single Molecules 32/0 Ex—
NBCM172Two-dimensional electronic spectroscopy 31/1 C+Ex1/1 C+Ex
NBCM026Experimental Technology in Molecular Spectroscopy 3—2/0 Ex
NBCM150Physical observation of nano-objects 52/1 C+Ex2/1 C+Ex
NBCM033Physical Principles of Photosynthesis 32/0 Ex—
NBCM156Chiroptic spectroscopy 3—2/0 Ex
NBCM067Quantum Optics I 52/1 C+Ex—
NFPL179Quantum Description of NMR 5—2/1 C+Ex
NBCM112Magnetic Resonance Methods in Biophysics 4—3/0 Ex
NBCM051Molecular Dynamics and Monte Carlo Methods 52/1 C+Ex—
NBCM008Molecular and Cell Biology for Biophysicist 43/0 Ex—
NBCM181Molecular dynamics — calculations of free energy 31/2 MC1/2 MC
NBCM114Optical Microscopy and Selected Imaging Techniques in Biophysics 3—2/0 Ex
NBCM316Computer Modelling of Biomolecules 41/2 C+Ex1/2 C+Ex
NTMF002Advanced Quantum Theory 63/1 C+Ex—
NFPL185Advanced High Resolution NMR Spectroscopy 52/1 C+Ex—
NBCM179Advanced methods of optical spectroscopy 4—3/0 Ex
NBCM158Practical aspects of experimental data treatment 31/1 Ex—
NBCM103Practical Course in Experimental Methods of Biophysics and Chemical Physics II 7—0/5 MC
NBCM098X-ray and Electron Structure Analysis of Biomolecules and Macromolecules 32/0 Ex—
NOOE012Scattering Methods in Optical Spectroscopy 3—2/0 Ex
NOOE015Seminar 2—0/1 C
NFPL186Seminar on High Resolution NMR Spectroscopy 30/2 C0/2 C
NFPL003Synthetic Problems of Quantum Theory 3—2/0 C
NPRF005UNIX and LINUX for Physicists 32/0 C—
NBCM159Introduction to Computer Control of Experiment 4—1/2 MC
NBCM308Introduction to Protein Structure Studies 3—2/0 Ex
NBCM115Scientific Photography and Related Imaging Techniques 31/1 Ex—
NBCM102Fundamentals of Classical Radiometry and Photometry 32/0 Ex—
NBCM042Fundamentals of Energy Transfer in Molecular Systems II 3—2/0 Ex

3.2 State Final Exam

Necesary conditions for taking the state final exam

– earning at least 120 credits during the course of the study
– passing all compulsory courses
– obtaining at least 25 credits for elective courses from the set I 
– obtaining at least 15 credits for elective courses from the set II
– submission of a completed master’s thesis by the submission deadline

Requirements for the oral part of the state final exam

A Common requirements

1 Quantum theory and statistical physics of molecules and molecular systems (one question in the state exam)

– Antisymmetry of wave function, exchange interaction.
– Born - Oppenheimer and adiabatic approximation.
– Hydrogen molecule. Atomic and molecular orbitals.
– LCAO method and valence bond method, classification of electron levels, Hückel method.
– One-particle approximation, Hartree and Hartree - Fock equations, Roothaan equations.
– Fundamentals of density functional theory, Hohenberg-Kohn theorems.
– Introduction to methods of configuration interaction, coupled clusters and perturbation theory, basic equations and properties, Brillouin theorem.
– Pauli and Dirac equations. Spin-orbital and spin-spin interaction.
– Orbital and spin magnetic moment and their interactions with external fields.
– Quantization of electromagnetic field, interaction of electromagnetic radiation with molecules. Fermi's golden rule.
– Absorption, stimulated and spontaneous emission. Dipole approximation, selection rules.
– Force fields in molecular systems.
– Standard statistical ensembles and distributions, ergodic theorem.
– Monte Carlo method.
– Classical molecular dynamics.
– Liouville equation.
– Density matrix. Wigner density.
– Standard quantum statistical distributions.
– Evolution of the density matrix (Liouville-von Neumann equation).
– Quantum master equation, reduced densities.

2 Experimental methods of biophysics and chemical physics (one question in the state exam)

– Sources, detectors and spectrum analyzers in optical spectroscopy.
– Interaction of optical radiation with an isolated molecule. Selection rules for electronic, vibrational and rotational optical transitions.
– Methods and applications of electron absorption spectroscopy. Excitation and probing method.
– Methods and applications of vibrational absorption spectroscopy.
– Methods of elastic, dynamic and Brillouin scattering and their applications.
– Raman scattering, measurement methods and their applications.
– Use of polarized radiation and its analysis in optical spectroscopy. Linear and circular dichroism, emission anisotropy.
– Principles and basic concepts of luminescence (types of luminescence, Jablonsky diagram, kinetics, quantum yield, lifetimes, Franck-Condon principle).
– Influence of intermolecular interactions on luminescence parameters (environmental influence, resonant energy transfer, emission quenching).
– Single-molecular spectroscopy. Influence of interaction with the environment on the shape of the spectral line.
– Measurement of stationary and time-resolved luminescence.
– Scattering and diffraction of X-rays, electrons and neutrons.
– Principles of basic diffraction methods. Symmetry and structure of crystals and their determination from the diffraction pattern.
– Electron microscopy, atomic force microscopy and scanning tunneling microscopy.
– Mass spectrometry.
– Nuclear magnetic resonance (NMR): principle, experimental setup, excitation and signal detection, basic pulse sequence.
– High resolution NMR of organic substances in liquids: interpretation of spectra.
– Electron paramagnetic resonance: principle, experimental setup, application.
– Separation methods (centrifugation, chromatography, electrophoresis).

B Specialization Experimental biophysics and chemical physics

The third question of the state exam is chosen from two thematic areas, which the student chooses according to his focus.

1 Biochemistry and molecular biology

– Composition and structure of basic biomolecules (nucleic acids, proteins, carbohydrates).
– Glycolysis and glycolytic reactions. Anaerobic degradation of sugars. Cori cycle.
– Aerobic degradation of sugars. Formation of acetylcoenzyme A.
– The citrate cycle and its amorphous nature. Oxidative phosphorylation.
– Biological membranes, selective permeability of biological membranes, types of transport through the biological membrane.
– Structure of bacterial and eukaryotic cells, cell division, cell cycle.
– DNA arrangement in cells, structure and function of chromosomes, chromatin and nucleosomes, centromere and telomere functions, histones, epigenetic inheritance and prions.
– Genetic information processing, DNA replication, RNA transcription and modification, RNA world, prokaryotic and eukaryotic translation.
– Basic principles of gene expression regulation, prokaryotic and eukaryotic transcription initiation regulation, gene silencing.
– Mutations and mutagenesis, DNA damage and repair of damaged DNA, correction of errors caused by DNA replication.
– Methods of studying DNA and gene expression, genetic engineering, fluorescent proteins.

2 Optical spectroscopy and biophysics of photosynthesis

– Fluorescent labels and probes, fluorescent proteins, protein fluorescence.
– Nonlinear methods of Raman scattering (HRS, SRS, CARS), Raman optical activity (ROA).
– Advanced techniques of Raman spectroscopy (SERS, CRM, DCDR).
– Generation and characterization of femtosecond pulses. Fundamentals of 2DES spectroscopy.
– Nonlinear optical phenomena and their applications in optical spectroscopy.
– High spectral resolution methods. Low temperature spectroscopy.
– Transmission and quenching of excitation in photosynthetic antennas.
– Charge distribution and transfer in low- and high-potential reaction centers.
– Electron transfer through the photosynthetic membrane, phosphorylation, comparison with the respiratory membrane.
– Carbon fixation in photosynthesis.
– Biophysical methods of investigation and measurement of photosynthesis (variable fluorescence, gasometry, photoacoustic spectroscopy).

3 Structural methods

– Temperature oscillations and their influence on diffraction recording. Patterson's function and its use in solving crystal structures.
– Methods for solving the phase problem of structural analysis.
– Structural factor and Friedel's law. Preferred orientation of crystallites - texture.
– Comparison, construction and use of transmission and scanning electron microscopes.
– Principles of sample preparation for TEM and SEM. Mechanism of image formation in TEM and SEM
– Electric and magnetic moments of atomic nuclei, energy in electric and magnetic fields, the phenomenon of nuclear magnetic resonance (NMR). Nuclear paramagnetism, relaxation processes.
– High resolution NMR spectroscopy in liquid and solid phase: spin Hamiltonian, types of interactions and their manifestations in spectra, high resolution methods in solid phase.
– One- and multidimensional pulse NMR: concept, basic pulse sequences, use of coherent polarization transfer and nuclear Overhauser effect.
– MR imaging: instrumentation, the principle of achieving spatial resolution, methods of contrast, special applications (angiography, fMRI, MRI spectroscopy).
– Electron spin (paramagnetic) resonance: continuous and pulse methodology of experiment, spin Hamiltonian, interactions and their manifestations in spectra.

B Specialization Theoretical biophysics and chemical physics

The third question of the state exam is chosen from two thematic areas, which the student chooses according to his focus.

1 Quantum chemistry

– Comparison of restricted and unrestricted Hartree-Fock equations and their properties.
– Configuration interaction methods, formulation and characteristics.
– Application of perturbation theory to the calculation of correlation energy, Møller-Plesset method.
– Coupled cluster method, excitation operators, equations and basic properties.
– Conceptual density functional theory - chemical potential, hardness and softness of electron density, Fukui function; time-dependent theory.
– Weak intermolecular interactions; multipole approximation.

2 Molecular dynamics and statistics

– Numerical propagators derived from the Liouville operator.
– Algorithms for pressure and temperature control. Fixation and restriction of degrees of freedom.
– Non-equilibrium molecular dynamics.
– Molecular mechanics, parameterization of force fields.
– Methods of molecular simulations – accounting for non-binding interactions, analysis of trajectories.
– Stochastic processes (Langevin dynamics, normal and anomalous diffusion).
– Stochastic quantum dynamics.
– Entropy in nonequilibrium processes (Boltzmann H-theorem, Jarzynski and fluctuation theorems).

3 Advanced theoretical spectroscopy

– Symmetry in quantum mechanics (quantum numbers, block diagonalization of Hamiltonian).
– Symmetry in the spectroscopy of atoms and molecules (selection rules, allowed and forbidden transitions, reduction of symmetry in external electromagnetic fields).
– Scattering of photons by atomic systems (Rayleigh, Raman, resonant and Thomson scattering).
– Radiative correction to atomic spectra (Lamb shift, self energy of electron and photon).
– Absorption line-shape (linear response theory, bath correlation function).
– Perturbation theory for time-resolved nonlinear spectroscopy (pump probe method, photon echo).
 

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