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63. Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteinsArtem Badasyan, Sh. A. Tonoyan, Matjaž Valant, Jože Grdadolnik, 2021, original scientific article Abstract: Studies of biopolymer conformations essentially rely on theoretical models that are routinely
used to process and analyze experimental data. While modern experiments allow study of
single molecules in vivo, corresponding theories date back to the early 1950s and require an
essential update to include the recent significant progress in the description of water. The
Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet
explicit model of water-polypeptide interactions that transforms into the equivalent implicit
description after performing the summation of solvent degrees of freedom in the partition
function. Here we show that our model fits very well to the circular dichroism experimental
data for both heat and cold denaturation and provides the energies of inter- and intra-
molecular H-bonds, unavailable with other processing methods. The revealed delicate
balance between these energies determines the conditions for the existence of cold dena-
turation and thus clarifies its absence in some proteins. Keywords: protein folding, cold denaturation, water, Zimm-Bragg model Published in RUNG: 06.05.2021; Views: 2187; Downloads: 15 Link to full text This document has many files! More... |
64. Covalent Organic Polymers and Frameworks for Fluorescence-Based SensorsTina Škorjanc, Dinesh Shetty, Matjaž Valant, 2021, review article Keywords: fluorescence, sensors, covalent organic polymers, covalent organic frameworks, quenching, ions, explosives Published in RUNG: 05.05.2021; Views: 2360; Downloads: 221 Link to full text This document has many files! More... |
65. Paramagnetic intrinsic point defects in alkali phosphate glasses : unraveling the P[sub]3 center origin and local environment effectsLuigi Giacomazzi, Nikita S. Shcheblanov, Layla Martin-Samos, Mikhail E. Povarnitsyn, Shinji Kohara, Matjaž Valant, Nicolas Richard, Nadege Ollier, 2021, original scientific article Keywords: oxygen, electron paramagnetic resonance spectroscopy, phosphates, amorphous materials, defects Published in RUNG: 04.05.2021; Views: 2767; Downloads: 0 This document has many files! More... |
66. Electronic properties of phases in the quasi-binary Bi[sub]2Se[sub]3-Bi[sub]2S[sub]3 systemZipporah Rini Benher, Sandra Gardonio, Mattia Fanetti, Paolo Moras, Asish K. Kundu, Chiara Bigi, Matjaž Valant, 2021, original scientific article Abstract: We explored the properties of the quasi-binary Bi2Se3–Bi2S3 system over a wide compositional range. X-ray diffraction analysis demonstrates that rhombohedral crystals can be synthesized within the solid solution interval 0–22 mol% Bi2S3, while at 33 mol% Bi2S3 only orthorhombic crystals are obtained. Core level photoemission spectroscopy reveals the presence of Bi3+, Se2− and S2− species and the absence of metallic species, thus indicating that S incorporation into Bi2Se3 proceeds prevalently through the substitution of Se with S. Spin- and angle-resolved photoemission spectroscopy shows that topological surface states develop on the surfaces of the Bi2Se3−ySy (y ≤0.66) rhombohedral crystals, in close analogy with the prototypical case of Bi2Se3, while the orthorhombic crystals with higher S content turn out to be trivial semiconductors. Our results connect unambiguously the phase diagram and electronic properties of the Bi2Se3–Bi2S3 system. Keywords: topological insulator, quasi-binary Bi2Se3-Bi2S3 system, electronic properties Published in RUNG: 29.03.2021; Views: 2286; Downloads: 0 This document has many files! More... |
67. The finite size effects and two-state paradigm of protein foldingArtem Badasyan, Matjaž Valant, Jože Grdadolnik, Vladimir N. Uversky, 2021, original scientific article Abstract: The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding Keywords: protein folding, two-state model, size scaling, thermodynamic cooperativity Published in RUNG: 24.02.2021; Views: 2192; Downloads: 66 Link to full text This document has many files! More... |
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69. Spremljanje, ugotavljanje in zagotavljanje kakovosti: : poročilo za študijsko leto 2019/2020 : Univerza v Novi Gorici, Fakulteta za znanosti o okoljuIztok Arčon, Blaž Belec, Marina Artico, Tea Stibilj Nemec, Maja Terčon, Matjaž Valant, Aljaž Rener, JANA BLEGUŠ, treatise, preliminary study, study Keywords: samoevalvacijsko poročilo Published in RUNG: 23.12.2020; Views: 2735; Downloads: 65 Full text (3,81 MB) |
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