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21.
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem Badasyan, invited lecture at foreign university

Abstract: 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.
Found in: osebi
Keywords: helix-coil transition, water-polypeptide interactions
Published: 13.03.2019; Views: 1497; Downloads: 0
.pdf Fulltext (78,48 KB)

22.
Perehod spiral'-klubok v kol'cevyh zamkiutyh DNK
Artem Badasyan, 2002, master's thesis

Found in: osebi
Published: 20.03.2019; Views: 1672; Downloads: 0
.pdf Fulltext (137,83 KB)

23.
OMPC model' i uporjadočenija biopolimerov
Lusine Arutjunjan, 2019, master's thesis

Found in: osebi
Published: 30.05.2019; Views: 1493; Downloads: 0
.pdf Fulltext (2,24 MB)

24.
DNA-CNT Physisorption
Artem Badasyan, invited lecture at foreign university

Found in: osebi
Keywords: DNA, CNT, zipper model, physisorption
Published: 28.01.2020; Views: 965; Downloads: 0
.pdf Fulltext (416,43 KB)

25.
Statistical mechanics of DNA-nanotube adsorption
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem Badasyan, 2019, other component parts

Abstract: 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.
Found in: osebi
Keywords: DNA-CNT physisorption, zipper model
Published: 28.01.2020; Views: 1129; Downloads: 0
.pdf Fulltext (515,48 KB)

26.
27.
Statistical mechanics of DNA adsorption on a carbon nanotube
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem Badasyan, 2020, published scientific conference contribution abstract

Abstract: The attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aro- matic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between them. With the goal to provide the theoretical support to numerous technologies on the basis of DNA-CNT hybrids, we propose a Hamiltonian formulation for the zipper model that accounts for relevant interactions and allows for the processing of experimental data, which has awaited an available theory for a decade.
Found in: osebi
Keywords: DNA, CNT
Published: 22.05.2020; Views: 894; Downloads: 47
.pdf Fulltext (2,96 MB)

28.
Statistical mechanics of DNA-nanotube adsorption
Artem Badasyan, Yevgeni S. Mamasakhlisov, Davit Khechoyan, Sh. A. Tonoyan, 2020, original scientific article

Abstract: Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNTs) and the aromaticnucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, aphenomenon related to hybridization. We propose a Hamiltonian formulation for the zipper model that accountsfor the DNA-CNT interactions and allows for the processing of experimental data, which has awaited an availabletheory for a decade.
Found in: osebi
Keywords: Carbon nanotubes, desoxyribonucleic acid, physisorption
Published: 30.06.2020; Views: 959; Downloads: 0
.pdf Fulltext (1,21 MB)

29.
Water reveals non-Arrhenius kinetics in protein folding experiments
Artem Badasyan, 2020, published scientific conference contribution abstract (invited lecture)

Abstract: Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo- ries are based on coarse-grained parameters, that include assumptions regarding the underlying kinetics. If such assumptions are incorrect, the theoretical expressions, used to process the experimental data, will not fit. I report on one such case we have met within the application of Zimm-Bragg [1] theory to process folding experiments, and discuss the reasons and consequences. Studies of relaxation phenomena in glass-forming liquids by default account for the shift in temperature by some value, corresponding to the glass formation temperature, .In particular, temperature shift appears in hydrated proteins because of the presence of partially glassy states giving rise to non- Arrhenius relaxation times log τ ~ [2]. A phenomenological approach was suggested by Adam and Gibbs as early as in 1965 to describe the sudden increase of viscosity and the slowing down of the collective modes in super-cooled liquids as the temperature is approaching[3]. The key idea of Adam-Gibbs theory was to consider the supercooled liquid as a set of clusters (cooperatively rearranging regions) of different sizes that change with temperature, giving rise to the shift in re- laxation time. The temperature shift factor is present in many theories describing properties of water. Thus, Truskett and Dill had to include the Adamm-Gibbs temperature shift into their simple analytical model of water to achieve the agreement with experimental data on the tem- perature dependence of self-diffusion coefficient [4]. Later, Schiro and Weik have summarised recent in vitro and in silico experimental results regarding the role of hydration water in the onset of protein structural dy- namics, and have reported the presence of super-Arrhenius relaxation region above the ”protein dynamic transition” temperature [4]. Recently, Mallamace et al have used the Adam-Gibbs theory in their NMR meas- urements of protein folding-unfolding in water [4] and to rationalise the complicated pressure-temperature diagrams in these glass-forming systems. Motivated by the considerations above, and taking into account the relationship between the unimolecular rate of folding in water and the relaxation time 45 , we introduce the tem- perature shift into the formulas used to fit experimental data on hydrated polypeptides. By doing so we resolve the paradox and complete the new method of processing the Circular Dichroism ex- perimental data on protein folding
Found in: osebi
Keywords: water, protein folding, non-Arrhenius kinetics
Published: 20.07.2020; Views: 849; Downloads: 45
.pdf Fulltext (2,35 MB)

30.
Modelling DNA adsorption on CNT
Artem Badasyan, Yevgeni S. Mamasakhlisov, 2020, published scientific conference contribution abstract

Abstract: Due to the attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) a reversible adsorption (physisorption) between them takes place. A large number of technologies are based on DNA-CNT hybrids [1], and thus require the theoretical support. Modelling this phenomenon in terms of Statistical Mechanics became recently possible, thanks to the Hamiltonian formulation of the zipper model [2].
Found in: osebi
Keywords: DNA, CNT, physisorption
Published: 22.09.2020; Views: 747; Downloads: 0
.pdf Fulltext (22,13 MB)

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