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52. Growth mechanism and structure of electrochemically synthesized dendritic polymethylsilane moleculesAndraž Mavrič, Artem Badasyan, Gregor Mali, Matjaž Valant, 2017, original scientific article Abstract: The study of an electrochemical synthesis of polymethylsilane from trifunctional trichloro-
methylsilane monomers identified a single polymerization pathway involving reduction of the
monomer to silyl anions and their addition to the growing polymer. The sizes of the synthesized
macromolecules, measured with dynamic light scattering, are much larger than the theoretical
size estimated for an ideal dendrimer. The reason for this, found by NMR analysis, is in a large
number of branching irregularities (defects) contained in the molecular structure, which can be
described as a hyperbranched dendritic polymer. Theoretical estimates of sizes for an ideal
dendrimer were corrected assuming a branching defect is a cavity with the volume of one
monomer. Appropriateness of the theoretical and experimental models was confirmed with a
good quantitative agreement between the experimental densities and the theoretically calculated
values.
Keywords: Polymethylsilane
Dendritic polymer
Electropolymerization
Published in RUNG: 20.03.2017; Views: 4924; Downloads: 19
 Full text (705,04 KB) |
53. Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein FoldingArtem Badasyan, invited lecture at foreign university Abstract: Biophysics is the area of research, devoted to the studies of physical problems related to living systems. Animal cell is the smallest unit of an organism and mainly contains water solutions of structurally inhomogeneous polymers of biological origin: polypeptides (proteins) and polynucleotides (DNA, RNA). Statistical physics of macromolecules allows to describe the conformations of both synthetic and bio-polymers and constitutes the basis of Biophysics. During the talk I will report on the biophysical problems I have solved with numerical simulations (Langevin-based Molecular Dynamics of Go-like protein folding model and Monte Carlo with Wang-Landau sampling) and analytical studies of spin models (formula evaluation by hand, enforced with computer algebra systems). The direct connections with the theory of phase transitions, algebra of non-commutative operators and decorated spin models will be elucidated.
Keywords: Biophysics, protein folding, helix-coil transition, spin models
Published in RUNG: 13.12.2016; Views: 6533; Downloads: 0
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55. WATER-POLYPEPTIDE INTERACTION IN CLASSICAL MODELS OF HELIX-COIL TRANSITIONKnarik Yeritsyan, 2016, undergraduate thesis Abstract: Zimm-Bragg model is the simplest to describe the conformational transitions in biopolymers and is regularly used for preocessing the experimental data. We review the model and its Hamiltonian definition with the goal to introduce the interaction with water into the picture. We show how modified ZB model with the account of water-polypeptide interactions allows to describe both cold denaturation and helix-coil transition and derive such the formula explicitly. The obtained theoretical expression for the helicity degree contains two independent parameters that can be fitted with the experimental data to determine the parameters of cold denaturation and helix-coil transition from a single fit and for a single set of experimental data.
Keywords: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Published in RUNG: 28.09.2016; Views: 8320; Downloads: 279
Full text (1,70 MB) |
56. Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?Artem Badasyan, invited lecture at foreign university Abstract: In spin models, that are applied to describe the conformational transitions in polymers, the number of spin orientations, that correspond to the disordered conformation, can be estimated using fundamental definitions of Statistical Physics. For instance, when considering alpha-helix to coil transition in polypeptides, the role of generalized coordinates is played by pairs of torsional angle, and the repeating unit populates different regions of that 2D contour map, depending on conformation. By scanning over all possible torsional angles, that do not violate the obvious limitations due to the excluded volume, the so-called Ramachandran map can be plotted, which is actually the phase space visualization for the helix-coil transition problem. The region of phase space, corresponding to the ordered, helical conformations, is much more limited, than the one, corresponding to all other (allowed) conformations. We can calculate the areas of these regions as Γhelix and Γcoil , and construct the ratio Q = Γcoil . Naturally, it can be interpreted as log(Q) = Scoil − Shelix = ΔS, the entropic cost of helix with respect to coil. To illustrate the importance of the entropic price of ordered conformation we report our recent results, that allowed to explain the peculiarity of phase diagrams of Intrinsically Disordered Proteins (IDP) out of larger Q-values, as compared to globular counterparts. In particular, it has been shown, that due to larger Q, the phase diagram of IDP is shifted towards higher temperatures.
Keywords: IDP, protein folding, phase diagram
Published in RUNG: 23.06.2016; Views: 5283; Downloads: 0
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