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31.
Statistical mechanics of DNA-nanotube adsorption
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem Badasyan, 2019, drugi sestavni deli

Opis: Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, a phenomenon related to hybridization. We propose a Hamiltonian formulation for the zipper model that accounts for the DNA-CNT interactions and allows for the processing of experimental data, which has awaited an available theory for a decade.
Ključne besede: DNA-CNT physisorption, zipper model
Objavljeno v RUNG: 28.01.2020; Ogledov: 3186; Prenosov: 0
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32.
DNA-CNT Physisorption
Artem Badasyan, predavanje na tuji univerzi

Ključne besede: DNA, CNT, zipper model, physisorption
Objavljeno v RUNG: 28.01.2020; Ogledov: 2696; Prenosov: 0
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33.
OMPC model' i uporjadočenija biopolimerov : diplomnaja rabota
Lusine Arutjunjan, 2019, magistrsko delo

Objavljeno v RUNG: 30.05.2019; Ogledov: 3612; Prenosov: 0
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34.
Perehod spiral'-klubok v kol'cevyh zamkiutyh DNK : magistrantskaja v'ipusknaja rabota
Artem Badasyan, 2002, magistrsko delo

Objavljeno v RUNG: 20.03.2019; Ogledov: 3877; Prenosov: 0
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35.
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem Badasyan, predavanje na tuji univerzi

Opis: The experimental studies of biopolymer conformations have reached an unprecedented level of detailization during the past decade and allow now to study single molecules in vivo [1]. Processing of experimental data essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the early 1960's and contain several unjustified assumptions, widely accepted at that time. Thus, the view on the conformational transitions in the polypeptides as a two-state process has very limited applicability because the all-or-none transition mechanism takes place only in short polypeptides with sizes comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is phenomenological and does not allow for a microscopic model for water; the implicit consideration of the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy difference on temperature can only be justified through the assumption of an ideal gas with a constant heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat and cold denaturation. On the example of several sets of experimental data we show, that our formula results in a significantly better fit, as compared to the existing approaches. Moreover, the application of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an information, inaccessible before.
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno v RUNG: 13.03.2019; Ogledov: 3428; Prenosov: 0
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36.
New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Artem Badasyan, Matjaž Valant, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: During the past decade the experimental studies of biopolymer conformations have reached an unprecedented level of detailization and allow to study single molecules in vivo [1]. Processing of experimental data essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the early 1960's and contain several unjustified assumptions, widely accepted at that time. Thus, the view on the conformational transitions in the polypeptides as a two-state process has very limited applicability because the all-or-none transition mechanism takes place only in short polypeptides with sizes comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is phenomenological and does not allow for a microscopic model for water; the implicit consideration of the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy difference on temperature can only be justified through the assumption of an ideal gas with a constant heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat and cold denaturation. On the example of several sets of experimental data we show, that our formula results in a significantly better fit, as compared to the existing approaches. Moreover, the application of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an information, inaccessible before. References [1] I. König, A. Zarrine-Afsar, M. Aznauryan, A. Soranno, B. Wunderlich, F. Dingfelder, J. C. Stüber, A. Plückthun, D. Nettels, B. Schuler, (2015), Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells/Nature Methods, 12, 773-779. [2] J. Seelig, H.-J. Schönfeld, (2016), Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy. Two-state model versus sequential unfolding/Quarterly Reviews of Biophysics, 49, e9, 1-24. [3] A.V. Badasyan, A. Giacometti, Y. Sh. Mamasakhlisov, V. F. Morozov, A. S. Benight, (2010), Microscopic formulation of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921. [4] B. H. Zimm, J. K. Bragg, (1959), Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains/Journal of Chemical Physics, 31, 526. [5] A. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y.Sh. Mamasakhlisov, V.F. Morozov, (2014), Unified description of solvent effects in the helix-coil transition/Physical Review E, 89, 022723. Corresponding author: Artem Badasyan (artem.badasyan@ung.si)
Ključne besede: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Objavljeno v RUNG: 22.10.2018; Ogledov: 4116; Prenosov: 0
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