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Do we really need water models in full, when it comes to studies of biopolymer conformations?
Artem Badasyan, 2014, objavljeni povzetek znanstvenega prispevka na konferenci

Najdeno v: ključnih besedah
Ključne besede: water, biopolymers, cold denaturation
Objavljeno: 22.01.2015; Ogledov: 2941; Prenosov: 18
URL Polno besedilo (0,00 KB)

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: ključnih besedah
Ključne besede: Zimm-Bragg model, conformational transitions in biopolymers, cold denaturation
Objavljeno: 28.09.2016; Ogledov: 4287; Prenosov: 185
.pdf Polno besedilo (1,70 MB)

Phenolic Contents and Postharvest Quality Changes of Norwegian ‘Mallard’ plums (Prunus domestica L.) as a Consequence of Delayed Time to Low Temperature Storage
Eivind Vangdal, Alena Gibalova, Branka Mozetič Vodopivec, 2012, objavljeni znanstveni prispevek na konferenci

Opis: During the picking season in the Norwegian plum production areas, the harvested plums are brought to cold storage in packing houses once or twice a day. Plums picked late in the afternoon may even not be cooled properly until the next day. The average time from picking until the plums are placed in a cold storage is approximately 8 hours. Previous reports have shown that delayed cooling of sweet cherries and apples reduced the fruits’ susceptibility to physiological or fungal decay. An experiment was performed in order to evaluate the impact of different delay-to-cold storage times (0, 5, 10, 15 and 25 hours) on quality and phenolic contents changes of Norwegian ‘Mallard’ plums during cold storage, transport, and retail in normal atmosphere (NA). The fruits (10 fruits in PE tray, n=3) were stored for 14 days at 1°C, followed by 3 days at 7°C and then for 4 days at 20°C. Fruit quality parameters (firmness, colour in CIE L, a*, b* colour space, weight, rot occurrence (%)) and total phenol and anthocyanin content were determined. Samples were analyzed just before cold storage and then after 14 days at 1°C, 3 days at 7°C, or 4 days at 20°C. Evaluation of results has shown that delay of cooling has a retarding effect on rot development during 20°C storage (post cold transport), weight loss and stimulates anthocyanin accumulation and colour changes to some extent. At the end of storage no effect on fruit firmness could be observed.
Najdeno v: ključnih besedah
Ključne besede: anthocyanins, total phenols, colour, rot, firmness, postharvest, plums, cold storage
Objavljeno: 11.11.2016; Ogledov: 2700; Prenosov: 0
.pdf Polno besedilo (268,22 KB)

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins
Jože Grdadolnik, Matjaž Valant, Sh. A. Tonoyan, Artem Badasyan, 2021, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Ključne besede: protein folding, cold denaturation, water, Zimm-Bragg model
Objavljeno: 06.05.2021; Ogledov: 235; Prenosov: 1
URL Polno besedilo (0,00 KB)
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