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21.
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
Artem V. 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.
Najdeno v: osebi
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno: 13.03.2019; Ogledov: 545; Prenosov: 0
.pdf Polno besedilo (78,48 KB)

22.
Perehod spiral'-klubok v kol'cevyh zamkiutyh DNK
Artem V. Badasyan, 2002, magistrsko delo

Najdeno v: osebi
Objavljeno: 20.03.2019; Ogledov: 613; Prenosov: 0
.pdf Polno besedilo (137,83 KB)

23.
OMPC model' i uporjadočenija biopolimerov
Lusine Arutjunjan, 2019, magistrsko delo

Najdeno v: osebi
Objavljeno: 30.05.2019; Ogledov: 488; Prenosov: 0
.pdf Polno besedilo (2,24 MB)

24.
DNA-CNT Physisorption
Artem V. Badasyan, predavanje na tuji univerzi

Najdeno v: osebi
Ključne besede: DNA, CNT, zipper model, physisorption
Objavljeno: 28.01.2020; Ogledov: 171; Prenosov: 0
.pdf Polno besedilo (416,43 KB)

25.
Statistical mechanics of DNA-nanotube adsorption
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem V. Badasyan, 2019, drugi članki ali sestavki

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.
Najdeno v: osebi
Ključne besede: DNA-CNT physisorption, zipper model
Objavljeno: 28.01.2020; Ogledov: 162; Prenosov: 0
.pdf Polno besedilo (515,48 KB)

26.
27.
Statistical mechanics of DNA adsorption on a carbon nanotube
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem V. Badasyan, 2020, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: 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.
Najdeno v: osebi
Ključne besede: DNA, CNT
Objavljeno: 22.05.2020; Ogledov: 11; Prenosov: 1
.pdf Polno besedilo (2,96 MB)

28.
Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?
Artem Badasyan, predavanje na tuji univerzi

Opis: 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.
Najdeno v: osebi
Ključne besede: IDP, protein folding, phase diagram
Objavljeno: 23.06.2016; Ogledov: 1772; Prenosov: 0
.pdf Polno besedilo (2,96 MB)
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29.
WATER-POLYPEPTIDE INTERACTION IN CLASSICAL MODELS OF HELIX-COIL TRANSITION
Knarik Yeritsyan, 2016, diplomsko delo

Opis: 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.
Najdeno v: osebi
Ključne besede: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Objavljeno: 28.09.2016; Ogledov: 2983; Prenosov: 145
.pdf Polno besedilo (1,70 MB)

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