195 research outputs found
Obdukcje są przyszłościowe. Antytraumatyczna sprawczość bohaterek powieści Anny Cieplak
No full textThe article discusses the literary work of Anna Cieplak, the author of contemporary novels focused on the social and economic challenges in provincial Poland. The analysis centers on the agency of female protagonists affected by traumatic experiences. Notably, these characters do not define themselves by their difficult pasts, and the narrative itself avoids introspection. In Lekki bagaż – which is subjected to the most detailed analysis in the article – as well as in Cieplak’s other novels, violence, although pervasive, does not play a central role in the plot. Instead, what proves crucial is the strategies of action employed by the protagonists, particularly women, who, despite adverse conditions, undertake efforts aimed at changing their circumstances.W artykule omówiono twórczość Anny Cieplak, autorki powieści oby- czajowych skupionych na społecznych i ekonomicznych wyzwaniach polskiej prowincji. Przeanalizowano kwestię sprawczości bohaterek dotkniętych trauma- tycznymi doświadczeniami. Co istotne, postaci te nie definiują się za sprawą swojej trudnej przeszłości, a w samej narracji powieściowej unika się introspekcji. Zarówno w fabule Lekkiego bagażu – poddanej w artykule najdokładniejszej ana- lizie – jak i innych powieści Cieplak przemoc, choć powszechna, nie odgrywa głównej roli. Kluczowe okazują się strategie działania bohaterów, a w szczegól- ności kobiet, które mimo trudnych warunków podejmują kroki z myślą o zmianie swojej sytuacji
Lattice tube model of proteins
No full textWe present a new lattice model for proteins that incorporates a tubelike anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins
Protein threading by learning
No full textBy using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins. These parameters provide a quantitative measure of the propensities of amino acids to be buried or exposed and to be in a given secondary structure and are a good starting point for solving both the threading and design problems
Optimal paths and growth processes
No full textInterfaces in systems with strong quenched disorder are fractal and are thus in a different universality class than the self-affine interfaces found in systems with weak quenched disorder. The geometrical properties of strands arising in loopless invasion percolation clusters, in loopless Eden growth clusters, and in the ballistic growth process are studied and their universality classes are identified
Amino acid classes and the protein folding problem
No full textWe present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic stability in and kinetic accessibility to the native state. A simple interpretation of the groups is obtained by eigenanalysis of the interaction matrix. (C) 2001 American Institute of Physics
What can one learn from experiments about the elusive transition state?
No full textWe present the results of an exact analysis of a model energy landscape of a protein to clarify the idea of the transition state and the physical meaning of the phi values determined in protein engineering experiments. We benchmark our findings to various theoretical approaches proposed in the literature for the identification and characterization of the transition state
Predicting the order in which contacts are broken during single molecule protein stretching experiments
No full textWe combine two methods to enable the prediction of the order in which contacts are broken under external stretching forces in single molecule experiments. These two methods are Gô-like models and elastic network models. The Gô-like models have shown remarkable success in representing many aspects of protein behavior, including the reproduction of experimental data obtained from atomic force microscopy. The simple elastic network models are often used successfully to predict the fluctuations of residues around their mean positions, comparing favorably with the experimentally measured crystallographic B-factors. The behavior of biomolecules under external forces has been demonstrated to depend principally on their elastic properties and the overall shape of their structure. We have studied in detail the muscle protein titin and green fluorescent protein and tested for ten other proteins. First, we stretch the proteins computationally by performing stochastic dynamics simulations with the Gô-like model. We obtain the force–displacement curves and unfolding scenarios of possible mechanical unfolding. We then use the elastic network model to calculate temperature factors (B-factors) and compare the slowest modes of motion for the stretched proteins and compare them with the predicted order of breaking contacts between residues in the Gô-like model. Our results show that a simple Gaussian network model is able to predict contacts that break in the next time stage of stretching. Additionally, we have found that the contact disruption is strictly correlated with the highest force exerted by the backbone on these residues. Our prediction of bond-breaking agrees well with the unfolding scenario obtained with the Gô-like model. We anticipate that this method will be a useful new tool for interpreting stretching experiments.This is the peer reviewed version of the following article: Sułkowska, Joanna I., Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, and Robert L. Jernigan. "Predicting the order in which contacts are broken during single molecule protein stretching experiments." Proteins: Structure, Function, and Bioinformatics 71, no. 1 (2008): 45-60, which has been published in final form at doi: 10.1002/prot.21652. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.</p
„Wykrzyknik ulicy:” Z Anną Cieplak o literaturze w działaniu, kryzysowych narracjach i zaangażowanej formie rozmawia Krzysztof Holvik
No full textKrzysztof Holvik’s conversation with Anna Cieplak focuses on the themes which include images of crises present in her novels, narratives of crisis, the issues concerning social engagement of literature, its interventionist nature and the risks involved. In her responses, the author of Ciało huty exposes the socio-political potential of the engaged form and the possibilities offered by its language, in the perception of which she unexpectedly finds inspiration inavant-garde poetry written under the sign of Julian Przyboś. All these themes are metaphorically intertwined to form the famous metaphor of a writer as “a street exclamation-ary,” giving the title to the entire conversation.Rozmowa z Anną Cieplak przeprowadzona przez Krzysztofa Holvika koncentruje się wokół kilku tematów przewodnich, do których należą narracje kryzysowe i obrazy kryzysów w powieściach autorki, a także zagadnienia społecznego zaangażowania literatury, jej interwencyjnego charakteru i związanego z nim ryzyka. W swoich odpowiedziach autorka Ciała huty eksponuje społeczno-polityczny potencjał zaangażowanej formy i możliwości, jakie daje jej język,w którego postrzeganiu inspiracją okazuje się nieoczekiwanie poezja awangardowa spod znaku Juliana Przybosia. Wszystkie te tematy metaforycznie splatają się w słynnej metaforze pisarza jako „wykrzyknika ulicy”, która nadaje tytuł całej rozmowie
Lattice Model For Rapidly Folding Protein-like Heteropolymers
No full textProtein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state, Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude, The evolutionary implications of our findings are discussed
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