We obtain the many-body hydrodynamic friction and mobility matrices describing the motion in a fluid of N hard-spheres with stick boundary conditions in the presence of a planar hard wall or free surface using ͑1͒ a multipole expansion of the hydrodynamic force densities induced on the spheres and ͑2͒ an image representation to account for the fluid boundary. The coupled multipole equations may be truncated at any order to give positive definite approximations to the exact friction and mobility matrices. An extension of the Bossis-Brady lubrication correction to the friction matrix is also discussed and included. The resulting method for computing the mobility matrix may be used for the Stokesian or Brownian dynamics simulation of N spheres subject to interparticle and external forces and imposed shear flow. We illustrate the method by performing Stokesian dynamics simulation of particles near a hard wall. The simulations exhibit the rapid convergence of the multipole truncation scheme including lubrication corrections.

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Complementary experimental techniques and ab initio calculations were used to determine the origin and nature of negative thermal expansion (NTE) in the archetype metal-organic framework MOF-5 (Zn(4)O(1,4-benzenedicarboxylate)(3)). The organic linker was probed by inelastic neutron scattering under vacuum and at a gas pressure of 175 bar to distinguish between the pressure and temperature responses of the framework motions, and the local structure of the metal centers was studied by X-ray absorption spectroscopy. Multi-temperature powder- and single-crystal X-ray and neutron diffraction was used to characterize the polymeric nature of the sample and to quantify NTE over the large temperature range 4-400 K. Ab initio calculations complement the experimental data with detailed information on vibrational motions in the framework and their correlations. A uniform and comprehensive picture of NTE in MOF-5 has been drawn, and we provide direct evidence that the main contributor to NTE is translational transverse motion of the aromatic ring, which can be dampened by applying a gas pressure to the sample. The linker motion is highly correlated rather than local in nature. The relative energies of different framework vibrations populated in MOF-5 are suggested by analysis of neutron diffraction data. We note that the lowest-energy motion is a librational motion of the aromatic ring which does not contribute to NTE. The libration is followed by transverse motion of the linker and the carboxylate group. These motions result in unit-cell contraction with increasing temperature.

As compared to 3d (first-row) transition metals, the 4d and 5d transition metals have much more diffuse valence orbitals. Quantum cooperative phenomena that arise due to changes in the way these orbitals overlap and interact, such as magnetoelasticity, are correspondingly rare in 4d and 5d compounds. Here, we show that the 6H-perovskite Ba(3)BiIr(2)O(9), which contains 5d Ir(4+) (S = 1/2) dimerized into isolated face-sharing Ir(2)O(9) bioctahedra, exhibits a giant magnetoelastic effect, the largest of any known 5d compound, associated with the opening of a spin-gap at T* = 74 K. The resulting first-order transition is characterized by a remarkable 4% increase in Ir-Ir distance and 1% negative thermal volume expansion. The transition is driven by a dramatic change in the interactions among Ir 5d orbitals, and represents a crossover between two very different, competing, ground states: one that optimizes direct Ir-Ir bonding (at high temperature), and one that optimizes Ir-O-Ir magnetic superexchange (at low temperature).

mWe describe the design philosophy, structure, and supporting tool kits of the NWChem computational chemistry package. The primary purpose of this effort was to develop efficient parallel algorithms for a broad range of methods commonly used in computational chemistry. To facilitate this, we developed a shared nonuniform access memory model which simplifies parallel programming while at the same time providing for portability across both distributed-and shared-memory machines. In addition to this specific focus on parallelization, a substantial effort has been made to simplify the general problem of large-scale software development, which is common to many research groups. We find that this simplification can be achieved through judicious use of ideas from the computer science field of software engineering in the design and implementation modeling software applications that provide 10-100 times more computing capability than has been available with conventional supercomputers. While increases in raw computing power alone will greatly expand the range of problems that can be treated by theoretical chemistry methods, a significant investment in new algorithms is needed

We describe an algorithm for performing Stokesian dynamics (SD) simulations of suspensions of arbitrary shape rigid particles with hydrodynamic interactions, modeled as rigid groups of spheres, the hydrodynamic mobility matrix of which is accurately computable by several established schemes for spheres. The algorithm is based on Stokesian rigid body equations of translational and rotational motion, which we have derived by an approach formally analogous to that of Newtonian rigid body dynamics. Particle orientation is represented in terms of Euler parameters (quaternion of rotation). This rigid body SD algorithm (RBSDA) complements recently described constraint SD algorithms [R. Kutteh, J. Chem. Phys. 119, 9280 (2003); R. Kutteh, Phys. Rev. E 69, 011406 (2004)], over which it offers the same computational advantages in imposing total rigidity that the basic rigid body molecular dynamics (MD) algorithm offers over constraint MD algorithms. We show that SD simulation results generated with the RBSDA, in bounded and unbounded geometries, agree very well with those from experiment and other SD and non-SD methods, and are numerically identical to those from a constraint SD algorithm, HSHAKE. Finally, for completeness we also describe a third (additional to the constraint SD and rigid body SD approaches) more traditional approach for SD simulations of arbitrary shape rigid particles modeled as rigid groups of spheres.

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Fast inactivation of the HERG potassium channel plays a critical role in normal cardiac function. Malfunction of these channels due to either genetic mutations or blockade by drugs leads to cardiac arrhythmias. An unusually long S5-P linker in the outer mouth of HERG is implicated in the fast inactivation mechanism. To examine the role of the S5-P linker in this inactivation mechanism, we study the permeation properties of the open and inactive states of a recent homology model of HERG. This model was constructed using the KcsA potassium channel as a template and contains specific conformations of the S5-P linker in the open and inactive states. We perform molecular dynamics simulations on the HERG model, followed by free energy, structural, and continuum electrostatics calculations. Our free energy calculations lead to selectivity results of the model channel (K + over Na + ) that are different in some respects from those of other potassium channels but consistent with experimental observations. Our structural results show that, in the inactive state, the S5-P linkers move closer to the channel axis, possibly causing a steric hindrance to permeating K + ions. Our electrostatics calculations reveal, in the inactive state, an electrostatic potential energy barrier of approximately 14 kT at the extracellular pore entrance, again sufficient to stop K + ion permeation through the pore. These results suggest that a steric and/or electrostatic plug mechanism contributes to inactivation in the HERG homology model.