1,494 research outputs found
Relative energetics and structural properties of zirconia using a self-consistent tight-binding model
We describe an empirical, self-consistent, orthogonal tight-binding model for
zirconia, which allows for the polarizability of the anions at dipole and
quadrupole levels and for crystal field splitting of the cation d orbitals.
This is achieved by mixing the orbitals of different symmetry on a site with
coupling coefficients driven by the Coulomb potentials up to octapole level.
The additional forces on atoms due to the self-consistency and polarizabilities
are exactly obtained by straightforward electrostatics, by analogy with the
Hellmann-Feynman theorem as applied in first-principles calculations. The model
correctly orders the zero temperature energies of all zirconia polymorphs. The
Zr-O matrix elements of the Hamiltonian, which measure covalency, make a
greater contribution than the polarizability to the energy differences between
phases. Results for elastic constants of the cubic and tetragonal phases and
phonon frequencies of the cubic phase are also presented and compared with some
experimental data and first-principles calculations. We suggest that the model
will be useful for studying finite temperature effects by means of molecular
dynamics.Comment: to be published in Physical Review B (1 march 2000
Solvated dissipative electro-elastic network model of hydrated proteins
Elastic netwok models coarse grain proteins into a network of residue beads
connected by springs. We add dissipative dynamics to this mechanical system by
applying overdamped Langevin equations of motion to normal-mode vibrations of
the network. In addition, the network is made heterogeneous and softened at the
protein surface by accounting for hydration of the ionized residues. Solvation
changes the network Hessian in two ways. Diagonal solvation terms soften the
spring constants and off-diagonal dipole-dipole terms correlate displacements
of the ionized residues. The model is used to formulate the response functions
of the electrostatic potential and electric field appearing in theories of
redox reactions and spectroscopy. We also formulate the dielectric response of
the protein and find that solvation of the surface ionized residues leads to a
slow relaxation peak in the dielectric loss spectrum, about two orders of
magnitude slower than the main peak of protein relaxation. Finally, the
solvated network is used to formulate the allosteric response of the protein to
ion binding. The global thermodynamics of ion binding is not strongly affected
by the network solvation, but it dramatically enhances conformational changes
in response to placing a charge at the active site of the protein
Molecular dynamics study of melatonin binding to homology modelled Mel1a G-protein coupled receptor
The Mel1a G-coupled Protein receptor (GPCR) was modelled using the I-Tasser online web service. All-atom molecular dynamics was used to improve the structure. The primary ligand melatonin was docked to the structure post molecular dynamics and structurally aligned to the X-ray crystallographic structures of the β2 adrenergic and rhodopsin GPCR’s, of the same family of proteins. A second set of all-atom molecular dynamics was undertaken with melatonin in the proposed active site which was parameterized ab initio in Gaussian16 to note any key conformational changes due to binding. The Mel1a GPCR becomes depolarized as a result of binding in the proposed active site by melatonin, based on Van der Waal interaction with amino acid residues on the extracellular side of the membrane (Ser176, Cys177, Tyr281 and Ser103)
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
- …