195 research outputs found
The relevance of ontological commitments
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.Comment: Submitted for peer-revie
Some lessons for us scientists (too) from the "Sokal affair"
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
Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2
We present an exhaustive study of more than 250 ab initio potential energy
surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries
(MCs) used are constructed as homo- and heterolevels involving possibly
different RHF and MP2 calculations for the geometry and the energy. The basis
sets used belong to a sample of 39 selected representants from Pople's
split-valence families, ranging from the small 3-21G to the large
6-311++G(2df,2pd). The reference PES to which the rest are compared is the
MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more
accurate PES of a dipeptide in the literature. The aim of the study presented
is twofold: On the one hand, the evaluation of the influence of polarization
and diffuse functions in the basis set, distinguishing between those placed at
1st-row atoms and those placed at hydrogens, as well as the effect of different
contraction and valence splitting schemes. On the other hand, the investigation
of the heterolevel assumption, which is defined here to be that which states
that heterolevel MCs are more efficient than homolevel MCs. The heterolevel
approximation is very commonly used in the literature, but it is seldom
checked. As far as we know, the only tests for peptides or related systems,
have been performed using a small number of conformers, and this is the first
time that this potentially very economical approximation is tested in full
PESs. In order to achieve these goals, all data sets have been compared and
analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che
Exact and efficient calculation of Lagrange multipliers in constrained biological polymers: Proteins and nucleic acids as example cases
In order to accelerate molecular dynamics simulations, it is very common to
impose holonomic constraints on their hardest degrees of freedom. In this way,
the time step used to integrate the equations of motion can be increased, thus
allowing, in principle, to reach longer total simulation times. The imposition
of such constraints results in an aditional set of Nc equations (the equations
of constraint) and unknowns (their associated Lagrange multipliers), that must
be solved in one way or another at each time step of the dynamics. In this work
it is shown that, due to the essentially linear structure of typical biological
polymers, such as nucleic acids or proteins, the algebraic equations that need
to be solved involve a matrix which is banded if the constraints are indexed in
a clever way. This allows to obtain the Lagrange multipliers through a
non-iterative procedure, which can be considered exact up to machine precision,
and which takes O(Nc) operations, instead of the usual O(Nc3) for generic
molecular systems. We develop the formalism, and describe the appropriate
indexing for a number of model molecules and also for alkanes, proteins and
DNA. Finally, we provide a numerical example of the technique in a series of
polyalanine peptides of different lengths using the AMBER molecular dynamics
package.Comment: 29 pages, 10 figures, 1 tabl
Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2
A general approach to the design of accurate classical potentials for protein
folding is described. It includes the introduction of a meaningful statistical
measure of the differences between approximations of the same potential energy,
the definition of a set of Systematic and Approximately Separable and Modular
Internal Coordinates (SASMIC), much convenient for the simulation of general
branched molecules, and the imposition of constraints on the most rapidly
oscillating degrees of freedom. All these tools are used to study the effects
of constraints in the Conformational Equilibrium Distribution (CED) of the
model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations
including electron correlation at the MP2 level to describe the system, and we
measure the conformational dependence of the correcting terms to the naive CED
based in the Potential Energy Surface (PES) without any simplifying assumption.
These terms are related to mass-metric tensors determinants and also occur in
the Fixman's compensating potential. We show that some of the corrections are
non-negligible if one is interested in the whole Ramachandran space. On the
other hand, if only the energetically lower region, containing the principal
secondary structure elements, is assumed to be relevant, then, all correcting
terms may be neglected up to peptides of considerable length. This is the first
time, as far as we know, that the analysis of the conformational dependence of
these correcting terms is performed in a relevant biomolecule with a realistic
potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included
Immunization of Real Complex Communication Networks
Most communication networks are complex. In this paper, we address one of the
fundamental problems we are facing nowadays, namely, how we can efficiently
protect these networks. To this end, we study an immunization strategy and
found that it works as good as targeted immunization, but using only local
information about the network topology. Our findings are supported with
numerical simulations of the Susceptible-Infected-Removed (SIR) model on top of
real communication networks, where immune nodes are previously identified by a
covering algorithm. The results provide useful hints in the way to design and
deploying a digital immune system.Comment: 6 pages. To appear in the European Physical Journal B (2006
Endogenous differential information in financial markets
We develop a two period general equilibrium model with incomplete financial markets and differential information. Making endogenous the traditional informational restriction on consumption, we allow agents to obtain information from physical and financial markets. Thus, the investment in financial promises and the trade of commodities in spot markets appear as natural channels to improve the information that an agent has about the realization of future states of nature.Incomplete Markets, Differential information, Enlightening equilibrium.
Efficient model chemistries for peptides. II. Basis set convergence in the B3LYP method
Pre-print version of an article published as Phil. Nat. 1:1-18 (2009), Copyright Excogitation & Innovation Laboratory, the published version can be found at http://www.eilab.org/pn/v1i1/20090003.htmSmall peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to correctly describe the conformational behaviour of small peptides constitutes an unavoidable first step. In this work, we present an study of several potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The PESs are calculated using the B3LYP density-functional theory (DFT) method, with Dunning’s basis sets cc-pVDZ, aug-cc-
pVDZ, cc-pVTZ, aug-cc-pVTZ, and cc-pVQZ. These calculations, whose cost amounts to approximately 10 years of computer time, allow us to study the basis set convergence of the B3LYP method for this model peptide. Also, we compare the B3LYP PESs to a previous computation at the MP2/6-311++G(2df,2pd) level, in order to assess their accuracy with respect to a higher level reference. All data sets have been analyzed according to a general framework which can be extended to other complex problems and which captures the nearness concept in the space of model chemistries (MCs).This work has been supported by the research projects DGA (Aragón Government, Spain) E24/3 and MEC (Spain) FIS2006-12781-C02-01. P. Echenique was supported by a MEC (Spain) postdoctoral contract
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