The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules

A method for generating angular forces around $\sigma$-bonded transition metal ions is generalized to treat $\pi$-bonded configurations. The theoretical approach is based on an analysis of a ligand-field Hamiltonian based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which however requires very little increased in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are $\sigma$- or $\pi$-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%. The resulting force field is used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when $\pi$-bonded ligands are present.Comment: Latex source, 9 postscript figure

Growth Velocities of Branched Actin Networks

The growth of an actin network against an obstacle that stimulates branching locally is studied using several variants of a kinetic rate model based on the orientation-dependent number density of filaments. The model emphasizes the effects of branching and capping on the density of free filament ends. The variants differ in their treatment of side vs. end branching and dimensionality, and assume that new branches are generated by existing branches (autocatalytic behavior) or independently of existing branches (nucleation behavior). In autocatalytic models, the network growth velocity is rigorously independent of the opposing force exerted by the obstacle, and the network density is proportional to the force. The dependence of the growth velocity on the branching and capping rates is evaluated by a numerical solution of the rate equations. In side-branching models, the growth velocity drops gradually to zero with decreasing branching rate, while in end-branching models the drop is abrupt. As the capping rate goes to zero, it is found that the behavior of the velocity is sensitive to the thickness of the branching region. Experiments are proposed for using these results to shed light on the nature of the branching process.Comment: 6 figure

Kinetics of coherent order-disorder transition in Al3ZrAl_3 Zr

Within a phase field approach which takes the strain-induced elasticity into account, the kinetics of the coherent order-disorder transition is investigated for the specific case of $Al_3 Zr$ alloy. It is shown that a microstructure with cubic $L1_2$ precipitates appears as a transient state during the decomposition of a homogeneous disordered solid solution into a microstructure with tetragonal $DO_{23}$ precipitates embedded into a disordered matrix. At low enough temperature, favored by a weak internal stress, only $L1_2$ precipitates grow in the transient microstructure preceding nucleation of the $DO_{23}$ precipitates that occurs exclusively at the interface of the solid solution with the $L1_2$ precipitates. Analysis of microstructures at nanoscopic scale shows a characteristic rod shape for the $DO_{23}$ precipitates due to the combination of their tetragonal symmetry and their large internal stress.Comment: 2 postscript figures and 1 JPG pag

Density-Matrix functional theory of strongly-correlated lattice fermions

A density functional theory (DFT) of lattice fermion models is presented, which uses the single-particle density matrix gamma_{ij} as basic variable. A simple, explicit approximation to the interaction-energy functional W[gamma] of the Hubbard model is derived from exact dimer results, scaling properties of W[gamma] and known limits. Systematic tests on the one-dimensional chain show a remarkable agreement with theBethe-Ansatz exact solution for all interaction regimes and band fillings. New results are obtained for the ground-state energyand charge-excitation gap in two dimensions. A successful description of strong electron correlations within DFT is achieved.Comment: 15 pages, 6 figures Submitted to PR

Interaction energy functional for lattice density functional theory: Applications to one-, two- and three-dimensional Hubbard models

The Hubbard model is investigated in the framework of lattice density functional theory (LDFT). The single-particle density matrix $\gamma_{ij}$ with respect the lattice sites is considered as the basic variable of the many-body problem. A new approximation to the interaction-energy functional $W[\gamma]$ is proposed which is based on its scaling properties and which recovers exactly the limit of strong electron correlations at half-band filling. In this way, a more accurate description of $W$ is obtained throughout the domain of representability of $\gamma_{ij}$, including the crossover from weak to strong correlations. As examples of applications results are given for the ground-state energy, charge-excitation gap, and charge susceptibility of the Hubbard model in one-, two-, and three-dimensional lattices. The performance of the method is demonstrated by comparison with available exact solutions, with numerical calculations, and with LDFT using a simpler dimer ansatz for $W$. Goals and limitations of the different approximations are discussed.Comment: 25 pages and 8 figures, submitted to Phys. Rev.

First-principles study of the polar O-terminated ZnO surface in thermodynamic equilibrium with oxygen and hydrogen

Using density-functional theory in combination with a thermodynamic formalism we calculate the relative stability of various structural models of the polar O-terminated (000-1)-O surface of ZnO. Model surfaces with different concentrations of oxygen vacancies and hydrogen adatoms are considered. Assuming that the surfaces are in thermodynamic equilibrium with an O2 and H2 gas phase we determine a phase diagram of the lowest-energy surface structures. For a wide range of temperatures and pressures we find that hydrogen will be adsorbed at the surface, preferentially with a coverage of 1/2 monolayer. At high temperatures and low pressures the hydrogen can be removed and a structure with 1/4 of the surface oxygen atoms missing becomes the most stable one. The clean, defect-free surface can only exist in an oxygen-rich environment with a very low hydrogen partial pressure. However, since we find that the dissociative adsorption of molecular hydrogen and water (if also the Zn-terminated surface is present) is energetically very preferable, it is very unlikely that a clean, defect-free (000-1)-O surface can be observed in experiment.Comment: 10 pages, 4 postscript figures. Uses REVTEX and epsf macro

Development of a tight-binding potential for bcc-Zr. Application to the study of vibrational properties

We present a tight-binding potential based on the moment expansion of the density of states, which includes up to the fifth moment. The potential is fitted to bcc and hcp Zr and it is applied to the computation of vibrational properties of bcc-Zr. In particular, we compute the isothermal elastic constants in the temperature range 1200K < T < 2000K by means of standard Monte Carlo simulation techniques. The agreement with experimental results is satisfactory, especially in the case of the stability of the lattice with respect to the shear associated with C'. However, the temperature decrease of the Cauchy pressure is not reproduced. The T=0K phonon frequencies of bcc-Zr are also computed. The potential predicts several instabilities of the bcc structure, and a crossing of the longitudinal and transverse modes in the (001) direction. This is in agreement with recent ab initio calculations in Sc, Ti, Hf, and La.Comment: 14 pages, 6 tables, 4 figures, revtex; the kinetic term of the isothermal elastic constants has been corrected (Eq. (4.1), Table VI and Figure 4

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.Comment: 43 pages, including 17 figure

Towards wide-scale adoption of open science practices: the role of open science communities

Multivariate analysis of psychological dat