Project description:The weak slab interface controls long-term subduction dynamics. A weak hydrous layer at the slab interface promotes mechanical decoupling between the forearc mantle and the subducting slab and converts a hot forearc mantle to a cold mantle. Often referred to as a cold nose, the cold forearc mantle, plays a key role in the transition from subduction infancy to mature subduction. This study was the first to numerically demonstrate the self-consistent formation of a weak hydrous layer with permeability anisotropy based on the Southwest Japan subduction zone case, where transition-related geological features were present. Our models showed that mechanical decoupling by spontaneous downdip growth of the weak hydrous layer created a cold nose by converting a hot forearc mantle to a cold mantle. The emergence of a cold nose explained the migration of the forearc-to-arc volcanic front, expressed as the formation of mid-Miocene forearc high-magnesium andesite and Quaternary arc adakite. Furthermore, the weak hydrous layer providing a pathway for free-water transport toward the mantle wedge tip elucidates slab/mantle-derived geochemical components in deep groundwater as well as large S-wave delay times and non-volcanic seismic tremors in the forearc.
Project description:A lattice model based on polymer self-consistent field theory is developed to predict the equilibrium statistics of arbitrary polymer networks. For a given network topology, our approach uses moment propagators on a lattice to self-consistently construct the ensemble of polymer conformations and cross-link spatial probability distributions. Remarkably, the calculation can be performed "in the dark", without any prior knowledge on preferred chain conformations or cross-link positions. Numerical results from the model for a test network exhibit close agreement with molecular dynamics simulations, including when the network is strongly sheared. Our model captures nonaffine deformation, mean-field monomer interactions, cross-link fluctuations, and finite extensibility of chains, yielding predictions that differ markedly from classical rubber elasticity theory for polymer networks. By examining polymer networks with different degrees of interconnectivity, we gain insight into cross-link entropy, an important quantity in the macroscopic behavior of gels and self-healing materials as they are deformed.
Project description:Despite decades of progress, an understanding of unconventional superconductivity still remains elusive. An important open question is about the material dependence of the superconducting properties. Using the quasiparticle self-consistent GW method, we re-examine the electronic structure of copper oxide high-Tc materials. We show that QSGW captures several important features, distinctive from the conventional LDA results. The energy level splitting between d(x(2)-y(2)) and d(3z(2)-r(2)) is significantly enlarged and the van Hove singularity point is lowered. The calculated results compare better than LDA with recent experimental results from resonant inelastic xray scattering and angle resolved photoemission experiments. This agreement with the experiments supports the previously suggested two-band theory for the material dependence of the superconducting transition temperature, Tc.
Project description:Field-theoretical method is efficient in predicting assembling structures of polymeric systems. However, it's challenging to generalize this method to study the polymer/nanoparticle mixture due to its multi-scale nature. Here, we develop a new field-based model which unifies the nanoparticle description with the polymer field within the self-consistent field theory. Instead of being "ensemble-averaged" continuous distribution, the particle density in the final morphology can represent individual particles located at preferred positions. The discreteness of particle density allows our model to properly address the polymer-particle interface and the excluded-volume interaction. We use this model to study the simplest system of nanoparticles immersed in the dense homopolymer solution. The flexibility of tuning the interfacial details allows our model to capture the rich phenomena such as bridging aggregation and depletion attraction. Insights are obtained on the enthalpic and/or entropic origin of the structural variation due to the competition between depletion and interfacial interaction. This approach is readily extendable to the study of more complex polymer-based nanocomposites or biology-related systems, such as dendrimer/drug encapsulation and membrane/particle assembly.
Project description:We present an approach that enables us to simultaneously access structure and dynamics of a multidomain protein in solution. Dynamic domain arrangements are experimentally determined by combining self-consistent networks of distance distributions with known domain structures. Local structural dynamics are correlated with the global arrangements by analyzing networks of time-resolved single-molecule fluorescence parameters. The strength of this hybrid approach is shown by an application to the flexible multidomain protein Hsp90. The average solution structure of Hsp90's closed state resembles the known X-ray crystal structure with Angstrom precision. The open state is represented by an ensemble of conformations with interdomain fluctuations of up to 25 Å. The data reveal a state-specific suppression of the submillisecond fluctuations by dynamic protein-protein interaction. Finally, the method enables localization and functional characterization of dynamic elements and domain interfaces.
Project description:X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.
Project description:Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties.
Project description:Adiabatic connection models (ACMs), which interpolate between the limits of weak and strong interaction, are powerful tools to build accurate exchange-correlation functionals. If the exact weak-interaction expansion from the second-order perturbation theory is included, a self-consistent implementation of these functionals is challenging and still absent in the literature. In this work, we fill this gap by presenting a fully self-consistent-field (SCF) implementation of some popular ACM functionals. While using second-order perturbation theory at weak interactions, we have also introduced new generalized gradient approximations (GGAs), beyond the usual point-charge-plus-continuum model, for the first two leading terms at strong interactions, which are crucial to ensure robustness and reliability. We then assess the SCF-ACM functionals for molecular systems and for prototypical strong-correlation problems. We find that they perform well for both the total energy and the electronic density and that the impact of SCF orbitals is directly connected to the accuracy of the ACM functional form. For the H2 dissociation, the SCF-ACM functionals yield significant improvements with respect to standard functionals also thanks to the use of the new GGAs for the strong-coupling functionals.
Project description:A two-dimensional class of mean-field models serving as a minimal frame to study long-range interaction in two space dimensions is considered. In the case of an anisotropic mixed attractive-repulsive interaction, an initially spatially homogeneous cold fluid is dynamically unstable and evolves towards a quasi-stationary state in which the less energetic particles get trapped into clusters forming a Bravais-like lattice, mimicking a crystalline state. Superimposed to this, one observes in symplectic numerical simulations a flux of slightly more energetic particles channeling through this crystalline background. The resultant system combines the rigidity features of a solid, as particles from a displaced core are shown to snap back into place after a transient, and the dynamical diffusive features of a liquid for the fraction of channeling and free particles. The combination of solid and liquid properties is numerically observed here within the classical context. The quantum transposition of the model may be experimentally reached using the latest ultracold atoms techniques to generate long-range interactions.
Project description:We developed a hybrid Monte Carlo self-consistent field technique to model physical gels composed of ABA triblock copolymers and gain insight into the structure and interactions in such gels. The associative A blocks of the polymers are confined to small volumes called nodes, while the B block can move freely as long as it is connected to the A blocks. A Monte Carlo algorithm is used to sample the node configurations on a lattice, and Scheutjens-Fleer self-consistent field (SF-SCF) equations are used to determine the change in free energy. The advantage of this approach over more coarse grained methods is that we do not need to predefine an interaction potential between the nodes. Using this MC-SCF hybrid simulation, we determined the radial distribution functions of the nodes and structure factors and osmotic compressibilities of the gels. For a high number of polymers per node and a solvent-B Flory-Huggins interaction parameter of 0.5, phase separation is predicted. Because of limitations in the simulation volume, we did however not establish the full phase diagram. For comparison, we performed some coarse-grained MC simulations in which the nodes are modeled as single particles with pair potentials extracted from SF-SCF calculations. At intermediate concentrations, these simulations gave qualitatively similar results as the MC-SCF hybrid. However, at relatively low and high polymer volume fractions, the structure of the coarse-grained gels is significantly different because higher-order interactions between the nodes are not accounted for. Finally, we compare the predictions of the MC-SCF simulations with experimental and modeling data on telechelic polymer networks from literature.