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Introduction to protein folding for physicists
Pablo Echenique
Physics , 2007, DOI: 10.1080/00107510701520843
Abstract: The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.
Testing for separability is hard
Federico Echenique
Computer Science , 2014,
Abstract: This paper shows that it is computationally hard to decide (or test) if a consumption data set is consistent with separable preferences.
Linfoma gástrico primario y hemorragia digestiva alta
M. Echenique-Elizondo
Revista Espa?ola de Enfermedades Digestivas , 2004,
Abstract:
Juxta-Ampullary Intraluminal Diverticulum and Acute Pancreatitis
Echenique-Elizondo M
JOP Journal of the Pancreas , 2004,
Abstract: CONTEXT: Acute pancreatitis is usually due to well-known causes, such as biliary lithiasis and alcohol consumption. Anatomic abnormalities may represent a less frequent but important etiological factor. CASE REPORT: The case of a 27 year old women complaining of acute pancreatitis associated with a large duodenal juxta-papillary diverticulum is presented. CONCLUSIONS: Anatomic causes of pancreatitis must be considered in the diagnosis of the etiology of acute pancreatitis.
The relevance of ontological commitments
Pablo Echenique-Robba
Physics , 2014,
Abstract: In this introductory note, I describe my particular view of the notion of ontological commitments as honest and pragmatic working hypotheses that assume the existence (out there) of certain entities represented by the symbols in our theory. I argue that this is not naive, in the sense that it does not entail the belief that the hypotheses could ever be proved to be true (or false), but it is nevertheless justified by the success and predictive power of the theory that contains the concepts assumed to exist. I also claim that the ontological commitments one holds (even if tacitly so) have a great influence on what kind of science is produced, how it is used, and how it is understood. Not only I justify this claim, but I also propose a sketch of a possible falsification of it. As a natural conclusion, I defend the importance of identifying, clarifying and making explicit one's ontological commitments if fruitful scientific discussions are to be had. Finally, I compare my point of view with that of some philosophers and scientists who have put forward similar notions.
Heating the coffee by looking at it. Or why quantum measurements are physical processes
Pablo Echenique-Robba
Physics , 2014,
Abstract: Using a very simple Gedankenexperiment, I remind the reader that (contrary to what happens in classical mechanics) the energy of a quantum system is inevitably increased just by performing (some) textbook measurements on it. As a direct conclusion, this means that some measurements require the expenditure of a finite amount of energy to be carried out. I also argue that this makes it very difficult to regard measurements as disembodied, immaterial, informational operations, and it forces us to look at them as physical processes just like any other one.
Some lessons for us scientists (too) from the "Sokal affair"
Pablo Echenique-Robba
Physics , 2013,
Abstract: In this little non-technical piece, I argue that some of the lessons that can be learnt from the bold action carried out in 1996 by the physicist Alan Sokal and typically known as the "Sokal affair" not only apply to some sector of the humanities (which was the original target of the hoax), but also (with much less intensity, but still) to the hardest sciences.
Shut up and let me think. Or why you should work on the foundations of quantum mechanics as much as you please
Pablo Echenique-Robba
Physics , 2013,
Abstract: If you have a restless intellect, it is very likely that you have played at some point with the idea of investigating the meaning and conceptual foundations of quantum mechanics. It is also probable (albeit not certain) that your intentions have been stopped on their tracks by an encounter with some version of the "Shut up and calculate" command. You may have heard that everything is already understood. That understanding is not your job. Or, if it is, it is either impossible or very difficult. Maybe somebody explained to you that physics is concerned with "hows" and not with "whys"; that whys are the business of "philosophy" ---you know, that dirty word. That what you call "understanding" is just being Newtonian; which of course you cannot ask quantum mechanics to be. Perhaps they also added some norms: The important thing a theory must do is predict; a theory must only talk about measurable quantities. It may also be the case that you almost asked "OK, and why is that?", but you finally bit your tongue. If you persisted in your intentions and the debate got a little heated up, it is even possible that it was suggested that you suffered of some type of moral or epistemic weakness that tend to disappear as you grow up. Maybe you received some job advice such as "Don't work in that if you ever want to own a house". I have certainly met all these objections in my short career, and I think that they are all just wrong. In this somewhat personal document, I try to defend that making sense of quantum mechanics is an exciting, challenging, important and open scientific endeavor. I do this by compulsively quoting Feynman (and others), and I provide some arguments that you might want to use the next time you confront the mentioned "opinions". By analogy with the anti-rationalistic Copenhagen command, all the arguments are subsumed in a standard answer to it: "Shut up and let me think"
Explicit factorization of external coordinates in constrained Statistical Mechanics models
Pablo Echenique,Ivan Calvo
Quantitative Biology , 2005, DOI: 10.1002/jcc.20499
Abstract: If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, we explicitly write the determinant of the mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule, general internal coordinates and arbitrary constraints, as a product of two functions; one depending only on the external coordinates that describe the overall translation and rotation of the system, and the other only on the internal coordinates. This work extends previous results in the literature, proving with full generality that one may integrate out the external coordinates and perform Monte Carlo simulations in the internal conformational space of macromolecules. In addition, we give a general mathematical argument showing that the factorization is a consequence of the symmetries of the metric tensors involved. Finally, the determinant of the mass-metric tensor G is computed explicitly in a set of curvilinear coordinates specially well-suited for general branched molecules.
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
Pablo Echenique,J. L. Alonso
Physics , 2007, DOI: 10.1080/00268970701757875
Abstract: We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.
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