scholarly journals Learning protein folding and evolution with a snake puzzle

2016 ◽  
Author(s):  
Gonzalo S Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Protein Folding ◽  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Folding Kinetics ◽  
Structure Comparison ◽  
Contact Matrix ◽  
Supplementary Material ◽  
The Stability ◽  
High Level

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Overlap. It also allows a simple representation of misfolded conformations and their free energy. These concepts, in particular protein structure comparison and the stability of the native state with respect to unfolded and misfolded conformations, will motivate evolutionary questions. We address these questions by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

scholarly journals Learning protein folding and evolution with a snake puzzle

2016 ◽  
Author(s):  
Gonzalo S Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Protein Folding ◽  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Folding Kinetics ◽  
Structure Comparison ◽  
Contact Matrix ◽  
Supplementary Material ◽  
The Stability ◽  
High Level

We propose here a working unit for teaching basic concepts of protein folding and evolution centred around the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Overlap. It also allows a simple representation of misfolded conformations and their free energy. These concepts, in particular protein structure comparison and the stability of the native state with respect to unfolded and misfolded conformations, will motivate evolutionary questions. We address these questions by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

scholarly journals Learning structural bioinformatics and evolution with a snake puzzle

2016 ◽  
Vol 2 ◽  
pp. e100 ◽  
Author(s):  
Gonzalo S. Nido ◽  
Ludovica Bachschmid-Romano ◽  
Ugo Bastolla ◽  
Alberto Pascual-García
Keyword(s):  
Teaching Practice ◽  
Protein Structures ◽  
Simple Algorithm ◽  
Structural Bioinformatics ◽  
Data Availability ◽  
Folding Kinetics ◽  
Contact Order ◽  
Contact Matrix ◽  
Supplementary Material ◽  
High Level

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’) to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

Energy landscapes and solved protein–folding problems

2004 ◽  
Vol 363 (1827) ◽  
pp. 453-467 ◽  
Author(s):  
Peter G. Wolynes
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Structure Prediction ◽  
Energy Landscape ◽  
Protein Structures ◽  
Energy Landscapes ◽  
Folding Kinetics ◽  
Energy Functions ◽  
Energy Landscape Theory ◽  
Novel Proteins

Energy–landscape theory has led to much progress in protein folding kinetics, protein structure prediction and protein design. Funnel landscapes describe protein folding and binding and explain how protein topology determines kinetics. Landscape–optimized energy functions based on bioinformatic input have been used to correctly predict low–resolution protein structures and also to design novel proteins automatically.

scholarly journals A little walk from physical to biological complexity: protein folding and stability

2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Thermal Resistance ◽  
Protein Structures ◽  
Amino Acid Substitutions ◽  
Biological Complexity ◽  
Statistical Potentials ◽  
Bioinformatics Tools ◽  
The Stability ◽  
Boltzmann Law

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and the change of these quantities upon amino acid substitutions. These methods are based on knowledge-driven statistical potentials, derived from experimental protein structures using the inverse Boltzmann law.

Radiation Effects on Hollandite Ceramics developed for Radioactive Cesium Immobilization

2003 ◽  
Vol 792 ◽  
Author(s):  
V. Aubin ◽  
D. Caurant ◽  
D. Gourier ◽  
N. Baffier ◽  
S. Esnouf ◽  
...  
Keyword(s):  
Radiation Effects ◽  
Liquid Waste ◽  
Fission Products ◽  
Radioactive Cesium ◽  
Radioactive Liquid Waste ◽  
Epr Spectrum ◽  
Paramagnetic Resonance ◽  
Γ Radiation ◽  
The Stability ◽  
High Level

ABSTRACTProgress on separating the long-lived fission products from the high level radioactive liquid waste (HLW) has led to the development of specific host matrices, notably for the immobilization of cesium. Hollandite (nominally BaAl2Ti6O16), one of the main phases constituting Synroc, receives renewed interest as specific Cs-host wasteform. The radioactive cesium isotopes consist of short-lived Cs and Cs of high activities and Cs with long lifetime, all decaying according to Cs+→Ba2++e- (β) + γ. Therefore, Cs-host forms must be both heat and (β,γ)-radiation resistant. The purpose of this study is to estimate the stability of single phase hollandite under external β and γ radiation, simulating the decay of Cs. A hollandite ceramic of simple composition (Ba1.16Al2.32Ti5.68O16) was essentially irradiated by 1 and 2.5 MeV electrons with different fluences to simulate the β particles emitted by cesium. The generation of point defects was then followed by Electron Paramagnetic Resonance (EPR). All these electron irradiations generated defects of the same nature (oxygen centers and Ti3+ ions) but in different proportions varying with electron energy and fluence. The annealing of irradiated samples lead to the disappearance of the latter defects but gave rise to two other types of defects (aggregates of light elements and titanyl ions). It is necessary to heat at relatively high temperature (T=800°C) to recover an EPR spectrum similar to that of the pristine material. The stability of hollandite phase under radioactive cesium irradiation during the waste storage is discussed.

scholarly journals Computing the Exact Number of Similarity Classes in the Longest Edge Bisection of Tetrahedra

Mathematics ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1447
Author(s):  
Jose P. Suárez ◽  
Agustín Trujillo ◽  
Tania Moreno
Keyword(s):  
Data Structure ◽  
Stability Condition ◽  
Open Problem ◽  
Integer Arithmetic ◽  
Exact Number ◽  
Similarity Class ◽  
The Stability ◽  
High Level ◽  
The Cost

Showing whether the longest-edge (LE) bisection of tetrahedra meshes degenerates the stability condition or not is still an open problem. Some reasons, in part, are due to the cost for achieving the computation of similarity classes of millions of tetrahedra. We prove the existence of tetrahedra where the LE bisection introduces, at most, 37 similarity classes. This family of new tetrahedra was roughly pointed out by Adler in 1983. However, as far as we know, there has been no evidence confirming its existence. We also introduce a new data structure and algorithm for computing the number of similarity tetrahedral classes based on integer arithmetic, storing only the square of edges. The algorithm lets us perform compact and efficient high-level similarity class computations with a cost that is only dependent on the number of similarity classes.

Features of pubertal patients with schizophrenia neurocognitive profile

2017 ◽  
Vol 41 (S1) ◽  
pp. S430-S431
Author(s):  
Y. Barylnik ◽  
S. Pakhomova ◽  
D. Samoylova ◽  
J. Abrosimova ◽  
E. Kolesnichenko ◽  
...  
Keyword(s):  
Stability Index ◽  
Neurocognitive Disorders ◽  
Motor Speed ◽  
Structuring Element ◽  
Test Part ◽  
Psychic Disorders ◽  
Competing Interest ◽  
Neurocognitive Profile ◽  
The Stability ◽  
High Level

Identifying the patterns of neurocognitive disorders in pubertal schizophrenia is actual.MethodsBenton Test of visual retention, methods of forward and reverse bills, Bourdon correction sample, Wechsler's subtests (subtest 11 – “Encryption”, subtest 12 – “Labyrinths” 1, 2, 3, 4, 5), Trail Creating a Test Part A.ResultsAll patients were divided into 3 groups. The first group (schizophrenia) and second group (other psychic disorders) showed the worst results than healthy subjects. Qualitative analysis of the “Benton Test” results showed similar variations of difficulty and types of errors in the subjects of the first and second groups – ignoring the number of the figure sides, as well as difficulties in the structuring element of the image corners. The “Methods of forward and reverse bills” demonstrated the fatigue and attention instability. “Bourdon test” showed a high level of the stability index (K = 0.09). Wechsler's subtest “Encryption B” obtained poor results, indicating a pathological decrease in visual-motor speed. During the subtest “Labyrinths 1, 2, 3, 4, 5” the subjects of first and second groups exceeded the allowable time limit, but the first group of schizophrenia patients allowed more blunders during pubertal study (ignored the walls of the maze, torn pencil despite the given instructions). The test groups 1 and 2 while passing “Trail Creating a Test Part A” have shown good results – job data did not cause difficulties and carried out in accordance with the specified instructions.ConclusionsNeurocognitive disorders allow to confirm the presence of morphological and functional brain changes when endogenous mental illness occurs.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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