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1.
The generalized model of polypeptide chain describing the helix-coil transition in biopolymers
Artem V. Badasyan, Yevgeni S. Mamasakhlisov, Artem V. Tsarukyan, Arsen V. Grigoryan, Vladimir F. Morozov, 2005, končno poročilo o rezultatih raziskav

Najdeno v: ključnih besedah
Ključne besede: biopolymers, helix-coil transition, conformation
Objavljeno: 25.04.2014; Ogledov: 1741; Prenosov: 40
URL Polno besedilo (0,00 KB)

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Packing patterns of silica nanoparticles on surfaces of armored polystyrene latex particles
Sara Fortuna, Catheline A. L. Colard, Stefan A. F. Bon, Alessandro Troisi, 2009, izvirni znanstveni članek

Opis: Fascinating packing patterns of identical spherical and discotic objects on curved surfaces occur readily in nature and science. Examples include C60 fullerenes,(1, 2)13-atom cuboctahedral metal clusters,(3) and S-layer proteins on outer cell membranes.(4) Numerous situations with surface-arranged objects of variable size also exist, such as the lenses on insect eyes, biomineralized shells on coccolithophorids,(5) and solid-stabilized emulsion droplets(6) and bubbles.(7) The influence of size variations on these packing patterns, however, is studied sparsely. Here we investigate the packing of nanosized silica particles on the surface of polystyrene latex particles fabricated by Pickering miniemulsion polymerization of submicrometer-sized armored monomer droplets. We are able to rationalize the experimental morphology and the nearest-neighbor distribution with the help of Monte Carlo simulations. We show that broadening of the nanoparticle size distribution has pronounced effects on the self-assembled equilibrium packing structures, with original 12-point dislocations or grain-boundary scars gradually fading out.
Najdeno v: ključnih besedah
Povzetek najdenega: ...patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles, nanoparticles, Pickering emulsion...
Ključne besede: packing patterns, silica, simulation, Monte Carlo, order, disorder, transition, armored particles, nanoparticles, Pickering emulsion
Objavljeno: 10.10.2016; Ogledov: 1490; Prenosov: 0
.pdf Polno besedilo (3,85 MB)

4.
Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein Folding
Artem V. Badasyan, predavanje na tuji univerzi

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...Biophysics, protein folding, helix-coil transition, spin models...
Ključne besede: Biophysics, protein folding, helix-coil transition, spin models
Objavljeno: 13.12.2016; Ogledov: 1380; Prenosov: 0
.pdf Polno besedilo (136,69 KB)

5.
CVD Growth of Molybdenum Diselenide Surface Structures with Tailored Morphology
M. Naeem Sial, Usman Muhammad, Binjie Zheng, Yanan Yu, Andraž Mavrič, Fangzhu Qing, Matjaž Valant, Zhiming M. Wang, 2018, izvirni znanstveni članek

Opis: Controllable atmospheric pressure CVD has been optimized to grow transition metal dichalcogenide MoSe2 with tunable morphology at 750 °C on a silicon substrate with a native oxide layer of 250 nm. Utilizing tetrapotassium perylene-3,4,9,10-tetracarboxylate (PTAS) as a seed promoter and varying the vertical distance between the substrate and the precursor MoO3, different morphologies of MoSe2 were achieved, including 2D triangles, hexagons, 3D pyramids and vertically aligned MoSe2 sheets. We find that the shape of MoSe2 is highly dependent upon the distance h between the substrate and the precursor. The change in the morphology is attributed to the confinement of vapor (MoO3 and Se) precursors and their concentrations due to the change in h. These results are helpful in improving our understanding about the factors which influence the morphology (shape evolution) and also the continuous growth of MoSe2 films.
Najdeno v: ključnih besedah
Povzetek najdenega: ...pressure CVD has been optimized to grow transition metal dichalcogenide MoSe2 with tunable morphology at...
Ključne besede: Transition metal dichalcogenides, 2D materials, Seed promotor, Chemical vapor deposition, Molybdenum diselenide
Objavljeno: 20.08.2018; Ogledov: 631; Prenosov: 0
.pdf Polno besedilo (2,68 MB)

6.
New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Artem V. 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)
Najdeno v: ključnih besedah
Povzetek najdenega: ...essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are...
Ključne besede: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Objavljeno: 22.10.2018; Ogledov: 465; Prenosov: 0
.pdf Polno besedilo (83,24 KB)

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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: ključnih besedah
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno: 13.03.2019; Ogledov: 355; Prenosov: 0
.pdf Polno besedilo (78,48 KB)

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