Prediction of the tertiary structure of a protein on a two-dimensional triangular lattice by a hybrid evolutionary algorithm

This work discusses the problem of forecasting the tertiary structure of a protein, based on its primary sequence. The problem is that science, with all its computing power and a set of experimental data, has not learned to build models that describe the process of protein molecule coagulation and predict the tertiary structure of a protein, based on its primary structure. However, it is wrong to assume that nothing is happening in this field of science. The regularities of folding (convolution) of the protein are known, methods for its modelling have been developed. Analysis of the current state of research in the field of these problems indicates the presence of shortcomings associated with the accuracy of forecasting and the time necessary to obtain the optimal solution. Consequently, the development of new computational methods, deprived of these shortcomings, seems relevant. In this work, the authors focused on the lattice model, which is a special case of the known hydrophobic-polar dill. protein conformation according to the chosen model, hybrid algorithms of cloning selection, differential are proposed. Since the processes of protein coagulation have not been fully understood, the researchers proposed several simplified models based on the physical properties of molecules and which leads to problems of combinatorial optimization. A hydrophobic-polar simplified model on the planar triangular lattice is chosen as a protein model. From the point of view of the optimization problem, the problem of protein folding comes down to finding a conformation with minimal energy. In lattice models, the conformation is represented as a non-self-cutting pathway. A hybrid artificial immune system in the form of a combination of clonal selection and differential evolution algorithms is proposed to solve this problem. The paper proposes a hybrid method and algorithm to solve the protein folding problem using the HP model on a planar triangular lattice. In this paper, a hybrid method and algorithm for solving the protein folding problem using the HP model on a planar triangular lattice are proposed. The developed hybrid algorithm uses special methods for encoding and decoding individuals, as well as the affinity function, which allows reducing the number of incorrect conformations (self-cutting solutions). Experimental studies on test hp-sequences were conducted to verify the effectiveness of the algorithm. The results of these experiments showed some advantages of the developed algorithm over other known methods. Experiments have been taught to verify the effectiveness of the proposed approach. The results labelled "Best" show the minimum energy values achieved over 30 runs, while the results labelled "Medium" show the robustness of the algorithm to achieve minima. Regarding robustness, the hybrid algorithm also offers an advantage, showing higher results. A comparative analysis of the performance results of the proposed algorithm on test sequences with similar results of other published methods allows us to conclude the high efficiency of the developed method. In particular, the result is more stable, and, in some cases, conformations with lower energy are obtained. Keywords: protein folding; hydrophobic-polar model; clonal selection; differential evolution; artificial immune systems; hydrophobic-polar model.

The Interaction of Cellulose Thin Films With Small Organic Molecules—Comparability of Two Inherently Different Methods

Paper is the material of choice for a large range of applications because it has many favorable environmental and economic characteristics. Especially in the packaging sector of dry goods and food products, paper has found unique applications. For that purpose, it has to fulfill certain requirements: Primarily it should protect the packaged goods. In order to ensure the compliance of a paper packaging, its interactions with the packaged goods should be investigated. Therefore, it is of utmost importance to understand how the paper interacts with chemicals of different nature and what factors influence these interactions—be that the nature of the paper or the characteristics of the substances. In this study, we investigated the surface interactions of cellulose thin films with n-decane and deuterated methanol using two different analytical methods: headspace solid-phase microextraction with gas chromatography and flame ionization detection (HS-SPME-GC/FID) and temperature-programmed desorption (TPD). Cellulose thin films were characterized with contact angle and FT-IR measurements and successfully applied as model systems for real paper samples. Regarding the interactions of the cellulose films with the model compounds, the two inherently different methods, HS-SPME-GC/FID and TPD, provide very comparable results. While the nonpolar n-decane was readily released from the cellulose films, the polar model compound deuterated methanol showed a strong interaction with the polar cellulose surface.

Toward a Foucauldian Genealogy of Video Game (Pre)history

This paper highlights the distortive nature of narrative models that are often employed in video game historiographies to produce captivating tales. More precisely, it argues against: the search for video games’ origin(s); the “chronological-teleological” model based on linear progressions; the “chronological-organic” narrative revolving around a biological-like evolution; the “epistemic breaks” structure based on radical transformations; the “bi-polar” model involving a dialectic of oppositions; and the “cyclical” narrative revolving around postmodern tropes of return, recycling, and retrofitting. In addition to explaining why the uncritical use of these emplotment techniques is problematic, this paper argues in favor of a Foucault-inspired genealogical approach which avoids the quest for the media’s origin(s) and articulates video game history around coexistence, overlaps, interferences, synergies, networks of influences, and discontinuities. This genealogical method also restores the missing inventors, devices, and games in historical records while highlighting the power relations that led to their omission in the first place.

Acute hemodynamic responses are not different for mono and multiarticular exercises for the same muscle group

Introduction: Different mechanical behaviors in resistance training can result in certain changes in the cardiovascular system. Objective: To verify the acute behavior of the main cardiovascular variables (heart rate, blood pressure, and double product) when performing resistance training with mono and multiarticular exercises. Methods: 10 male subjects participated in the study (26 ± 4 years; 81 ± 6 kg; 1.77 ± 2 m; 23 ± 1 kg / m2). They performed a test and retest for 8RM in the bench press and crucifix exercises on the machine. After the loads were outlined, they performed the intervention with the exercises, initially with a monoarticular activation containing two sets of 12 repetitions with 50% of the load acquired in the 8RM test of each exercise, using an interval of 60 seconds between one set and another. Additionally, three sets of 8 repetitions (80% 8RM) were performed with an interval between sets of 120 seconds. The execution speed was determined at a moderate level (2s for concentric, 2s for eccentric). It was measured before and during (series 1, series two, and series 3. Named as moments) heart rate exercises using POLAR, model RS800CX Multisport® and blood pressure using OMRON M6 (HEM-7001- E) ®. Then, the double product was calculated using the formula [HR (bpm) X SBP (mmHg)]. Results: In the heart rate analysis, there was an intra-condition difference for moments 1, 2, and 3 compared to rest (p <0.000). In the inter-condition comparison, no differences were observed for rest (p = 0.994) and for moments 1, 2 and 3 (p> 0.999). In systolic blood pressure, intra-conditions, differences were observed for moments 1, 2, and 3 compared to rest (p <0.000). In the inter-condition comparisons, there were no differences between rest (p> 0.999), moment 1 (p = 0.714), 2 (p = 0.999) and 3 (p> 0.999). For diastolic blood pressure, intra conditions, for bench press no significant differences were found for moments 1 (p = 0.331), 2 (p = 0.505) and 3 (p = 0.505) when compared to rest. In the same way it was for the crucifix, wherein the comparison with rest, no difference was observed in moments 1 (p = 0.849), 2 (p = 0.195) and 3 (p = 0.105). In the same sense, no difference was also observed in the comparisons between conditions for rest (p> 0.999), moment 1 (p = 0.999), 2 (p = 0.989) and 3 (p = 0.948). Finally, the double product in intra-condition comparisons found differences between moments 1, 2, and 3 compared to rest (p <0.000). However, in the inter-condition comparisons, no difference was observed at rest (p = 0.999), moment 1 (p = 0.868), 2 and 3 (p> 0.999). Conclusion: It is suggested that resistance training composed of mono and multi-joint exercises offers differences in hemodynamic responses but without differences between the types of mechanics applied by the exercises. Therefore, these results offer a partiality of what can happen with heart rate, blood pressure, and double product.

L’influenza de la Dialectique des “exercices spirituels” de Saint Ignace de Loyola nel pensiero di Jorge Mario Bergoglio

When in October 2016 I started working on my book Jorge Mario Bergoglio. An intellectual biography I did not have the slightest idea of ​​the importance played by the figure and work of Gaston Fessard in the formation of Bergoglio’s thought. There was nothing to suggest that Gaston Fessard could be a relevant author for the intellectual formation of the future Pope. I was struck by the polar and dialectical model of thought that animated him, the possibility of harmonizing opposites, of inviting concepts to a common table that apparently could not be approached, because it places them in a higher plane in which they find their synthesis. This paradigm, of the Church and of the Society of Jesus as complexio oppositorum, finds its verification, according to Bergoglio, in the way in which the Jesuits have achieved the inculturation of the faith in the indigenous peoples of Latin America. Bergoglio rereads Ignatius in the light of a dialectical model. As he will say in one of the interviews he gave me on the occasion of the writing of my book: “In Ignatian spirituality there is always this bipolar tension”. It is certainly an original, uncommon reading of Ignatius’s thought. It is the ideal factor that allows us to explain why Bergoglio, when in 1986 he went to Frankfurt to write his doctoral thesis, chose the Guardinian essay dedicated to the polar opposition. When I concluded my volume on the intellectual biography of the future Pontiff in February 2017, one element, however, remained obscure. Where, from which author had Bergoglio drawn his polar model? Where did your antinomic reading of Ignatian spirituality come from? Not by Guardini discovered philosophically in 1986. Francis indicated the starting point of his intellectual formation. The reading of Fessard’s La dialectique des Exercices spirituels de saint Ignace de Loyola, published in 1956, is the work that “ had a great influence “ on him. It is the work that clarifies Bergoglio’s antinomian thought, his subsequent ideal encounter with Guardini’s philosophy.

Self-moments stiffening effect and buckling strength of periodic Vierendeel beams

This paper deals with the buckling phenomenon of periodic Vierendeel beams. Closed-form solutions for critical loads and deformed shapes are presented. They are built by exploiting several auxiliary solutions obtained for the discrete periodic girder and for a geometrically nonlinear micro-polar equivalent model. In particular, the girder when subjected to sinusoidal self-equilibrated systems of inner bending moments (self-moments) is analysed. The corresponding results are used for solving the large-deflection equilibrium problem of the continuous equivalent model by means of the eigenfunction expansion technique. Girder buckling conditions are then defined in terms of kinematics of the micro-polar model: more precisely, they are attained when special distributions of self-moments, able to bend the continuous system without violating compatibility of shear strains, act in the girder. It is shown that these systems, neglected in the theories presented so far, have a significant stiffening effect on the buckling girder behaviour. Moreover, they are governed by the continuity equation for micro-rotations that is solved in closed form by the Galerkin method, with the micro-polar model eigenfunctions as basis functions. The accuracy of the proposed solutions is verified by comparing them with those achieved by a series of finite element girder models.

Microfluidic Chip-Based Induced Phase Separation Extraction as a Fast and Efficient Miniaturized Sample Preparation Method

Induced phase separation extraction (IPSE) is an efficient sample clean-up technique that can replace liquid-liquid extraction (LLE). The purpose of this study was to miniaturize IPSE by carrying it out in a microfluidic chip. An IPSE chip was designed and evaluated for its ability to separate and purify samples on a microscale. The 5 × 2 cm chip was fed with a solution of polar to non-polar model compounds in acetonitrile-water (1:1). In the 100 µm wide and 40 µm deep microchannels, the sample solution was efficiently separated into two immiscible phases by adding a hydrophobic solvent as inducer. Analytes present in the sample solution each migrated to their own favorable phase upon phase separation. After optimization, extraction and fractionation were easily and efficiently achieved. The behavior of analytes with a pH-dependent partitioning could be influenced by adjusting the pH of the sample solution. Scutellaria baicalensis extract, used in Traditional Chinese Medicine (TCM), was successfully separated in aglycones and glycosides. In this microscale system, the sample and solvent consumption is reduced to microliters, while the time needed for the sample pretreatment is less than one minute. Additionally, the extraction efficiency can reach up to 98.8%, and emulsion formation is avoided.

Tools for Shaping Stories? Visual Plot Models in a Sample of Anglo-American Advice Handbooks

This chapter examines the “storyology” in writing manuals, focusing on the verbal and the visual plot models in a corpus of sixteen mainstream creative writing handbooks on plot, novels, and screenplays, still in use today. We will focus on the prevalence of dramatic writing and the predominance of the “Mountain Model,” a model which combines earlier linear models, such as the “three-act structure,” “Field’s paradigm,” “Fichtean Curve,” “Freytag’s Pyramid,” and the polar model, built on the alternation of good and bad fortune, along with Joseph Campbell’s “Hero’s Journey.” The Mountain Model visualizes a concept of writing particularly suited for stories capable of being resolved within a limited time frame, combining the perspectives of protagonist and reader. While this model is usually presented as ideal and universal, changing the representation from a linear to a topographical model alters the kinds of plots which can be imagined.