Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure

Interacting Growth Walk on a honeycomb lattice

The Interacting Growth Walk (IGW) is a kinetic algorithm proposed recently for generating long, compact, self avoiding walks. The growth process in IGW is tuned by the so called growth temperature $T' = 1/(k_B \beta ')$. On a square lattice and at $T' = 0$, IGW is attrition free and hence grows indefinitely. In this paper we consider IGW on a honeycomb lattice. We take contact energy, see text, as $\epsilon=-|\epsilon|=-1$. We show that IGW at $\beta' =\infty$ ($T'=0$) is identical to Interacting Self Avoiding Walk (ISAW) at $\beta=\ln 4$ ($k_B T = 1/\ln 4=0.7213$). Also IGW at $\beta ' = 0$ ($T' = \infty$) corresponds to ISAW at $\beta = \ln 2$ ($k_B T= 1/ln 2 = 1.4427$). For other temperatures we need to introduce a statistical weight factor to a walk of the IGW ensemble to make correspondence with the ISAW ensemble.Comment: 3 pages, 1 figure, REVTEX fil

Exciton doublet in the Mott-Hubbard LiCuVO4_4 insulator identified by spectral ellipsometry

Spectroscopic ellipsometry was used to study the dielectric function of LiCuVO$_{4}$, a compound comprised of chains of edge-sharing CuO$_4$ plaquettes, in the spectral range (0.75 - 6.5) eV at temperatures (7-300) K. For photon polarization along the chains, the data reveal a weak but well-resolved two-peak structure centered at 2.15 and 2.95 eV whose spectral weight is strongly enhanced upon cooling near the magnetic ordering temperature. We identify these features as an exciton doublet in the Mott-Hubbard gap that emerges as a consequence of the Coulomb interaction between electrons on nearest and next-nearest neighbor sites along the chains. Our results and methodology can be used to address the role of the long-range Coulomb repulsion for compounds with doped copper-oxide chains and planes.Comment: 4 pages with 4 figures and EPAPS supplementary online material (3 pages with 4 figures), accepted in Phys. Rev. Let

Irreversible Processes in a Universe modelled as a mixture of a Chaplygin gas and radiation

The evolution of a Universe modelled as a mixture of a Chaplygin gas and radiation is determined by taking into account irreversible processes. This mixture could interpolate periods of a radiation dominated, a matter dominated and a cosmological constant dominated Universe. The results of a Universe modelled by this mixture are compared with the results of a mixture whose constituents are radiation and quintessence. Among other results it is shown that: (a) for both models there exists a period of a past deceleration with a present acceleration; (b) the slope of the acceleration of the Universe modelled as a mixture of a Chaplygin gas with radiation is more pronounced than that modelled as a mixture of quintessence and radiation; (c) the energy density of the Chaplygin gas tends to a constant value at earlier times than the energy density of quintessence does; (d) the energy density of radiation for both mixtures coincide and decay more rapidly than the energy densities of the Chaplygin gas and of quintessence.Comment: 8 pages, 1 figure, to be published in GR

Ground state of two unlike charged colloids: An analogy with ionic bonding

In this letter, we study the ground state of two spherical macroions of identical radius, but asymmetric bare charge ((Q_{A}>Q_{B})). Electroneutrality of the system is insured by the presence of the surrounding divalent counterions. Using Molecular Dynamics simulations within the framework of the primitive model, we show that the ground state of such a system consists of an overcharged and an undercharged colloid. For a given macroion separation the stability of these ionized-like states is a function of the difference ((\sqrt{N_{A}}-\sqrt{N_{B}})) of neutralizing counterions (N_{A}) and (N_{B}). Furthermore the degree of ionization, or equivalently, the degree of overcharging, is also governed by the distance separation of the macroions. The natural analogy with ionic bonding is briefly discussed.Comment: published versio

Band filling and interband scattering effects in MgB2_2: C vs Al doping

We argue, based on band structure calculations and Eliashberg theory, that the observed decrease of $T_c$ of Al and C doped MgB$_2$ samples can be understood mainly in terms of a band filling effect due to the electron doping by Al and C. A simple scaling of the electron-phonon coupling constant $\lambda$ by the variation of the density of states as function of electron doping is sufficient to capture the experimentally observed behavior. Further, we also explain the long standing open question of the experimental observation of a nearly constant $\pi$ gap as function of doping by a compensation of the effect of band filling and interband scattering. Both effects together generate a nearly constant $\pi$ gap and shift the merging point of both gaps to higher doping concentrations, resolving the discrepancy between experiment and theoretical predictions based on interband scattering only.Comment: accepted by PR