Maxim Yulikov: Catalogue data in Autumn Semester 2022

Name Dr. Maxim Yulikov
Inst. Mol. Phys. Wiss.
ETH Zürich, HCI F 231
Vladimir-Prelog-Weg 1-5/10
8093 Zürich
Telephone+41 44 632 31 18
DepartmentChemistry and Applied Biosciences

529-0053-00LPolymer Physics Methods for Unstructured Biomolecules3 credits2VM. Yulikov, G. Jeschke
AbstractThe course will provide the "polymer physics view" for the broad area of bio-polymers research. This will include simple and advanced concepts, forming the theoretical "language", critical overview of experimental methods, including the differences in characterization of synthetic and bio-polymers, concepts for modelling conformational ensembles of unstructured bio-polymers.
ObjectiveFrom the fundamental education point, this course will systematically overview the power of the thermodynamic description, and the interplay between the energy and the entropy for the phenomena that happen at the edge of near equivalence of the thermal energy and the inter-molecular interaction energy.

Due to complexity of the bio-molecular interactions, the most successful research approaches in the field of unstructured bio-polymers are based on a clever combination of several structural and spectroscopic methods.

Therefore, in this course, there will be a good opportunity to introduce the cross-validation analysis based on complimentary spectroscopic methods, to see examples from real research on different accuracy and different applicability ranges of experimental methods, and to discuss how very different spectroscopic data types can be combined to enhance the understanding of a bio-polymer system.
Content- Overview of unstructured bio-polymers and bio-polymers with unstructured domains.

- Overview of bio-molecular interactions and interactions to the solvent molecules: types of interactions, energy scales, time scales, length scales.

- Overview of spectroscopic methods to characterize the overall conformational properties of unstructured bio-polymers, the strength of their interactions, the peculiarities of their interactions at the atomic level (fluorescence methods, magnetic resonance methods, scattering methods, cross linking methods).

- Comparison of these methods in respect to their applicability range, sensitivity range, accuracy, type of the data.

- Thermodynamic concepts of bio-polymers, existing models for energy and entropy contributions: Flory theory for polymer chain conformational distribution, reversible gelation theory, electrochemical solvent effects, isotope effects, entropic effects for inhomogeneous distribution of interacting moieties over the polymer chain.

- Topics on nucleic acids: double helix vs. single strand stability, conformational ensembles, solvent interactions.

- Topics on unstructured proteins and protein domains: entropy contributions, reversible folding, crowding effects, liquid-liquid phase separation, RNA interactions, entropic terms in protein crystallization, entropic terms in reaction constants of interfering binding sites.

- Topics of polymer physics of carbohydrates.

- Site directed labeling of weakly interacting unstructured bio-molecules, disturbances, selection of reference states, interpretation of the data.

- Hybrid methods in studies of bio-polymers, their strength and challenges: accuracy and information content of different methods, ways to combine them, ways to model the bio-polymers based on hybrid spectroscopic data, ways to describe the broad conformational ensembles.
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesDecision-makingassessed