arXiv subjects

Pablo Echenique

Publications and source records attributed to Pablo Echenique.

24 records · Page 2Linked to original sources

arXiv2005

A physically meaningful method for the comparison of potential energy functions

In the study of the conformational behavior of complex systems, such as proteins, several related statistical measures are commonly used to compare two different potential energy functions. Among them, the Pearson's correlation coefficient r has no units and allows only semi-quantitative statements to be made. Those that do have units of energy and whose value may be compared to a physically relevant scale, such as the root mean square deviation (RMSD), the mean error of the energies (ER), the standard deviation of the error (SDER) or the mean absolute error (AER), overestimate the distance between potentials. Moreover, their precise statistical meaning is far from clear. In this article, a new measure of the distance between potential energy functions is defined which overcomes the aforementioned difficulties. In addition, its precise physical meaning is discussed, the important issue of its additivity is investigated and some possible applications are proposed. Finally, two of these applications are illustrated with practical examples: the study of the van der Waals energy, as implemented in CHARMM, in the Trp-Cage protein (PDB code 1L2Y) and the comparison of different levels of the theory in the ab initio study of the Ramachandran map of the model peptide HCO-L-Ala-NH2.

q-bio.QM↗

arXiv2005

Relevant distance between two different instances of the same potential energy in protein folding

In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two different instances of the same potential-energy function are used. When the two instances arise from the fact that different algorithms or different approximations are used, the distance herein defined may be used to evaluate the relative accuracy of the two methods. When the difference is due to a change in the free parameters of which the potential depends on, the distance can be used to quantify, in each region of parameter space, the robustness of the modeling to such a change and this, in turn, may be used to assess the significance of a parameters' fit. Both cases are illustrated with a practical example: the study of the Poisson-based solvation energy in the Trp-Cage protein (PDB code 1L2Y).

q-bio.BM↗

arXiv2005

Distance-d covering problems in scale-free networks with degree correlations

A number of problems in communication systems demand the distributed allocation of network resources in order to provide better services, sampling and distribution methods. The solution to these issues is becoming more challenging due to the increasing size and complexity of communication networks. We report here on an heuristic method that allows to find near-optimal solutions to the covering problem in real communication networks. The results show that the optimal allocation of resources strongly depends on the topology of the underlying networks. Whether a centralized or distributed design is to be used relies upon the degree correlations between connected vertices.

cond-mat.stat-mech↗

arXiv2004

Dynamics of jamming transitions in complex networks

We numerically investigate jamming transitions in complex heterogeneous networks. Inspired by Internet routing protocols, we study a general model that incorporates local traffic information through a tunable parameter. The results show that whether the transition from a low-traffic regime to a congested phase is of first or second order type is determined by the protocol at work. The microscopic dynamics reveals that these two radically different behaviors are due to the way in which traffic jams propagate through the network. Our results are discussed in the context of Internet dynamics and other transport processes that take place on complex networks and provide insights for the design of routing policies based on traffic awareness in communication systems.

cond-mat.stat-mech↗

arXiv2004

Improved routing strategies for Internet traffic delivery

We analyze different strategies aimed at optimizing routing policies in the Internet. We first show that for a simple deterministic algorithm the local properties of the network deeply influence the time needed for packet delivery between two arbitrarily chosen nodes. We next rely on a real Internet map at the autonomous system level and introduce a score function that allows us to examine different routing protocols and their efficiency in traffic handling and packet delivery. Our results suggest that actual mechanisms are not the most efficient and that they can be integrated in a more general, though not too complex, scheme.

cond-mat.other↗

arXiv2004

Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.

q-bio.BM↗