Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Carbon and nitrogen emissions from stored manure and cropped fields in irrigated mountain oases of Oman

Little is known about gaseous carbon (C) and nitrogen (N) emissions from traditional terrace agriculture in irrigated high mountain agroecosystems of the subtropics. In an effort towards filling this knowledge gap measurements of carbon dioxide (CO_2), methane (CH_4), ammonia (NH_3) and dinitrous oxide (N_2O) were taken with a mobile photoacoustic infrared multi-gas monitor on manure-filled PE-fibre storage bags and on flood-irrigated untilled and tilled fields in three mountain oases of the northen Omani Al Jabal al Akhdar mountains. During typical 9-11 day irrigation cycles of March, August and September 2006 soil volumetric moisture contents of fields dominated by fodder wheat, barley, oats and pomegranate ranged from 46-23%. While manure incorporation after application effectively reduced gaseous N losses, prolonged storage of manure in heaps or in PE-fibre bags caused large losses of C and N. Given the large irrigation-related turnover of organic C, sustainable agricultural productivity of oasis agriculture in Oman seems to require the integration of livestock which allows for several applications of manure per year at individual rates of 20 t dry matter ha^−1.

Measure Fields for Function Approximation

The computation of a piecewise smooth function that approximates a finite set of data points may be decomposed into two decoupled tasks: first, the computation of the locally smooth models, and hence, the segmentation of the data into classes that consist on the sets of points best approximated by each model, and second, the computation of the normalized discriminant functions for each induced class. The approximating function may then be computed as the optimal estimator with respect to this measure field. We give an efficient procedure for effecting both computations, and for the determination of the optimal number of components.

Evaluation of sets of oriented and non-oriented receptive fields as local descriptors

Local descriptors are increasingly used for the task of object recognition because of their perceived robustness with respect to occlusions and to global geometrical deformations. We propose a performance criterion for a local descriptor based on the tradeoff between selectivity and invariance. In this paper, we evaluate several local descriptors with respect to selectivity and invariance. The descriptors that we evaluated are Gaussian derivatives up to the third order, gray image patches, and Laplacian-based descriptors with either three scales or one scale filters. We compare selectivity and invariance to several affine changes such as rotation, scale, brightness, and viewpoint. Comparisons have been made keeping the dimensionality of the descriptors roughly constant. The overall results indicate a good performance by the descriptor based on a set of oriented Gaussian filters. It is interesting that oriented receptive fields similar to the Gaussian derivatives as well as receptive fields similar to the Laplacian are found in primate visual cortex.

Vector Fields

Exercises and solutions about vector fields. Diagrams for the questions are all together in the support.zip file, as .eps files

Fields of vision. Literature in the english language. 1.

Antología de la literatura en lengua inglesa desde los orígenes hasta la época contemporánea. Su objetivo es inculcar en los estudiantes el amor por la literatura y hacer que participen activamente en la experiencia del aprendizaje a través de: un examen a fondo del mundo literario en inglés basado en una selección equilibrada de autores y textos; una estructura modular en la que cada módulo corresponde a un período histórico / literario; una introducción a la apreciación de los textos literarios a través del análisis de las principales características de los géneros literarios; así como un enfoque flexible, que permite elaborar itinerarios modulares y realizar análisis de texto completo.

Fields of vision. Literature in the english language. 2.

Antología de la literatura en lengua inglesa desde los orígenes hasta la época contemporánea. Su objetivo es inculcar en los estudiantes el amor por la literatura y hacer que participen activamente en la experiencia del aprendizaje a través de: un examen a fondo del mundo literario en inglés basado en una selección equilibrada de autores y textos; una estructura modular en la que cada módulo corresponde a un período histórico / literario; una introducción a la apreciación de los textos literarios a través del análisis de las principales características de los géneros literarios; así como un enfoque flexible, que permite elaborar itinerarios modulares y realizar análisis de texto completo.

A scaled-down conference model for courses covering ever-changing fields in computer science undergraduate degree programs

Resumen tomado de la publicación

Guidelines for strategic national planning of training and education for museums, cultural heritage and related fields in Sweden and in international co-operation

The guidelines presented in this document are a preliminary strategy for establishing a comprehensive policy for the needs of training and education wiyhin the sector and adjoining areas, across fields of knowledge and professions concerned, on relevant levels and for the varies institutions and operators. The objective of these guidelines is to analysis the problems, objectives and goals for development of a far reaching system of educational and training programs and courses for museums, cultural heritage and related fields of activities. This objective comprises a close collaboration between museum, cultural heritage organizations and educating organizations, notably within universities and colleges, but also other kinds of educating bodies.

Museologial action's main fields

Museology has emerged and has been organised as a field of knowledge, precisely to frame the technical, theoretical and methodological aspects, regarding the constitution, implementation and evaluation of the processes that societies establish for the selection, treatment and extroversion of the memory indicators, transforming them into patrimonial references and projecting them into the constitutive fields of cultural heritage. It is therefore, one of the areas of knowledge that deals with the framing of heritage and their professionals are agents of memory education. The constitution of the parameters that define and delimit the museological action field has been outlined in the course of the centuries, if we consider the technical efforts related to the identification and organisation of collections, in addition to the curatorial treatment of specimens from nature, of objects, of the intangible heritage registers. The same length of elaboration is true if we evaluate the communication initiatives and of education of the senses.