LARGE SCALE SIMULATIONS OF COMPLEX SYSTEMS, CONDENSED MATTER AND FUSION PLASMA: Proceedings of the BIFI2008 International Conference: Large Scale Simulations of Complex Systems, Condensed Matter and Fusion Plasma
1071(2008); http://dx.doi.org/10.1063/1.3033357View Description Hide Description
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative behavior of the molecular subunits lining up to build chainlike macromolecules. Proteins experience conformational transitions related to thermodynamic phase transitions. For chains of finite length, an important difference of crossovers between conformational (pseudo)phases is, however, that these transitions are typically rather smooth processes, i.e., thermodynamic activity is not necessarily signalized by strong entropic or energetic fluctuations. Nonetheless, in order to understand generic properties of molecular structure‐formation processes, the analysis of mesoscopic models from a statistical physics point of view enables first insights into the nature of conformational transitions in small systems. Here, we review recent results obtained by means of sophisticated generalized‐ensemble computer simulations of minimalistic coarse‐grained models.
1071(2008); http://dx.doi.org/10.1063/1.3033358View Description Hide Description
The role of the divertor in a stellarator‐based fusion reactor is discussed, making emphasis on the flux‐expansion concept. In this context, the possibility of having a flux‐expansion divertor in TJ‐II is explored. As a first step, the three‐dimensional map of the particle flux has been estimated using the code ISDEP in two different plasma regimes. This full‐f Monte Carlo code computes the ion guiding‐centre trajectories. The particle trajectories rather than the field lines must be considered due to the fact that the typical ion orbits are pretty wide in comparison with the typical plasma lengths. Moreover the plasma electric field and the collisionality must be considered. We have chosen a configuration that presents flux expansion at given toroidal positions. We have estimated the three‐dimensional map of heat and particle fluxes and checked that it is possible to reduce them strongly by intersecting the trajectories at a given zone of the space. Future studies will include the development of ergodic zones to reduce the fluxes on the divertor plates.
1071(2008); http://dx.doi.org/10.1063/1.3033359View Description Hide Description
We present a detailed numerical study on the effects of adding quenched impurities to a three dimensional system which in the pure case undergoes a strong first order phase transition (specifically, the ferromagnetic/paramagnetic transition of the site‐diluted four states Potts model). We can state that the transition remains first‐order in the presence of quenched disorder (a small amount of it) but it turns out to be second order as more impurities are added. A tricritical point, which is studied by means of Finite‐Size Scaling, separates the first‐order and second‐order parts of the critical line. The results were made possible by a new definition of the disorder average that avoids the diverging‐variance probability distributions that arise using the standard methodology. We also made use of a recently proposed microcanonical Monte Carlo method in which entropy, instead of free energy, is the basic quantity.
Study on the stability of the Quadruplex DNA Structure formed by the human telomeric repeat sequence1071(2008); http://dx.doi.org/10.1063/1.3033361View Description Hide Description
Molecular Dynamics Simulations were performed on a quadruplex DNA structure formed by one folded single DNA strand with the sequence in presence of or ions. Starting coordinates were based on high resolution X‐ray structure crystallized in presence of ions. Molecular Dynamics simulations were carried out upon a quadruplex core region containing or The simulations were performed at 300 K and at 400 K. In all cases, the simulations show that these structures are very stable. This is supported by the results of the characteristic intramolecular distances monitored during the first nanoseconds after proper thermal equilibration of the structures at 300 or 400 K. Total time of simulations reached 20 nanoseconds.
1071(2008); http://dx.doi.org/10.1063/1.3033362View Description Hide Description
We introduce a new code of plasma transport based on evolving the Boltzmann equation in guiding center approximation where collisions has been taken into account. The spatial geometry is discretized using high order elements in space and a moment expansion in velocity space. First calculations with non‐evolving electric field agree with the particle code ISDEP
1071(2008); http://dx.doi.org/10.1063/1.3033363View Description Hide Description
New detailed models of the protein structures by means of a physical description at the atomic level have improved the possibilities to treat de novo computational protein design. The existing methods mostly rely on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence, in its optimal side‐chain configuration, on a given main‐chain structure. While the solvation entropy term is often taken implicitly, the conformational entropy stemming from alternative side‐chain arrangements is usually omitted (or not properly evaluated) since its computation is generally intractable.
A method recently proposed by the authors  incorporates such conformational entropy based on statistical mechanics principles. In this work we further test the protein design methodology, that we applied to the complete redesign of 27 proteins, and study how the entropy affects the ranking of the same sets of sequences at low and high temperatures. We also investigate how the new methodology affects the fraction of aminoacids of each kind that are found in solvent‐protected positions. Our results indicate that accounting for entropic contribution in the score function affects the outcome in a highly non‐trivial way, and might improve current computational design techniques based on protein stability. Indeed, ranking at low and high temperatures are, in general, weakly correlated, pointing out the importance of accounting for the entropy. We also notice that the free‐energy driven design yields sequences that differ in many positions from those obtained with the standard design, while the burial fraction for the aminoacids does not change much.
1071(2008); http://dx.doi.org/10.1063/1.3033364View Description Hide Description
We show here our work in structural prediction of protein‐protein interactions. Our computational docking methodology has two major components: the sampling of mutual orientations of the interacting molecules, and the scoring and clustering of these orientations for the identification of near‐native docking poses. Our procedure can generate a uniformly distributed set of rigid‐body docking poses, which can be easily extended to explore the flexibility of the side‐chains. The method is able to find near‐native orientations in line with other state‐of‐the‐art docking programs, and it has been successfully applied together with our pyDock scoring scheme in the most recent rounds of the CAPRI worl‐wide experiment (http://capri.ebi.ac.uk). We have also devised a new measure to compare rigid‐body docking poses based on angular distance (instead of RMSD), which describes the relative orientations of the two molecules in the different docking poses, as evaluated in a large benchmark of known protein‐protein cases. The low computational cost of this measure (as compared with the RMSD calculation) makes it ideal for clustering docking poses in a more effective way. The new docking angular index of similarity (DASI) can also be used to evaluate the validity of the docking predictions, when comparing with the X‐ray structures.
1071(2008); http://dx.doi.org/10.1063/1.3033356View Description Hide Description
The ion Drift Kinetic Equation (DKE) which describes the ion collisional transport is solved for the TJ‐II device plasmas. This non‐linear equation is computed by performing a mean field iterative calculation. In each step of the calculation, a Fokker‐Planck equation is solved by means of the Langevin approach: one million particles are followed in a realistic TJ‐II magnetic configuration, taking into account collisions and electric field. This allows to avoid the assumptions made in the usual neoclassical approach, namely considering radially narrow particle trajectories, diffusive transport, energy conservation and infinite parallel transport. As a consequence, global features of transport, not present in the customary neoclassical models, appear: non‐diffusive transport and asymmetries on the magnetic surfaces.