113 research outputs found
The Functional Form of Angular Forces around Transition Metal Ions in Biomolecules
A method for generating angular forces around -bonded transition
metal ions is generalized to treat -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
- or -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 -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
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 alloy. It is shown that a microstructure
with cubic precipitates appears as a transient state during the
decomposition of a homogeneous disordered solid solution into a microstructure
with tetragonal precipitates embedded into a disordered matrix. At
low enough temperature, favored by a weak internal stress, only
precipitates grow in the transient microstructure preceding nucleation of the
precipitates that occurs exclusively at the interface of the solid
solution with the precipitates. Analysis of microstructures at
nanoscopic scale shows a characteristic rod shape for the
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
Expansion algorithm for the density matrix
A purification algorithm for expanding the single-particle density matrix in
terms of the Hamiltonian operator is proposed. The scheme works with a
predefined occupation and requires less than half the number of matrix-matrix
multiplications compared to existing methods at low (90%)
occupancy. The expansion can be used with a fixed chemical potential in which
case it is an asymmetric generalization of and a substantial improvement over
grand canonical McWeeny purification. It is shown that the computational
complexity, measured as number of matrix multiplications, essentially is
independent of system size even for metallic materials with a vanishing band
gap.Comment: 5 pages, 4 figures, to appear in Phys. Rev.
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 with
respect the lattice sites is considered as the basic variable of the many-body
problem. A new approximation to the interaction-energy functional
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 is obtained throughout the domain of
representability of , 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 .
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 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 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
is compared to experiments. Implications for protein crystallization are
discussed.Comment: 43 pages, including 17 figure
- …