3,715 research outputs found
Thermodynamics of Na_8 and Na_{20} clusters studied with ab-initio electronic structure methods
We study the thermodynamics of Na_8 and Na_{20} clusters using
multiple-histogram methods and an ab initio treatment of the valence electrons
within density functional theory. We consider the influence of various electron
kinetic-energy functionals and pseudopotentials on the canonical ionic specific
heats. The results for all models we consider show qualitative similarities,
but also significant temperature shifts from model to model of peaks and other
features in the specific-heat curves. The use of phenomenological
pseudopotentials shifts the melting peak substantially (~ 50--100 K) when
compared to ab-initio results. It is argued that the choice of a good
pseudopotential and use of better electronic kinetic-energy functionals has the
potential for performing large time scale and large sized thermodynamical
simulations on clusters.Comment: LaTeX file and EPS figures. 24 pages, 13 figures. Submitted to Phys.
Rev.
Cyclic Density Functional Theory : A route to the first principles simulation of bending in nanostructures
We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) -- a
self-consistent first principles simulation method for nanostructures with
cyclic symmetries. Using arguments based on Group Representation Theory, we
rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems
can be reduced to a fundamental domain (or cyclic unit cell) augmented with
cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics
appearing in Kohn-Sham theory can be reduced to the fundamental domain
augmented with cyclic boundary conditions. By making use of this symmetry cell
reduction, we show that the electronic ground-state energy and the
Hellmann-Feynman forces on the atoms can be calculated using quantities defined
over the fundamental domain. We develop a symmetry-adapted finite-difference
discretization scheme to obtain a fully functional numerical realization of the
proposed approach. We verify that our formulation and implementation of Cyclic
DFT is both accurate and efficient through selected examples.
The connection of cyclic symmetries with uniform bending deformations
provides an elegant route to the ab-initio study of bending in nanostructures
using Cyclic DFT. As a demonstration of this capability, we simulate the
uniform bending of a silicene nanoribbon and obtain its energy-curvature
relationship from first principles. A self-consistent ab-initio simulation of
this nature is unprecedented and well outside the scope of any other systematic
first principles method in existence. Our simulations reveal that the bending
stiffness of the silicene nanoribbon is intermediate between that of graphene
and molybdenum disulphide. We describe several future avenues and applications
of Cyclic DFT, including its extension to the study of non-uniform bending
deformations and its possible use in the study of the nanoscale flexoelectric
effect.Comment: Version 3 of the manuscript, Accepted for publication in Journal of
the Mechanics and Physics of Solids,
http://www.sciencedirect.com/science/article/pii/S002250961630368
Hybrid Quantum Mechanical/ Molecular Mechanical Methods for Studying Energy Transduction in Biomolecular Machines
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems
Novel algorithms and high-performance cloud computing enable efficient fully quantum mechanical protein-ligand scoring
Ranking the binding of small molecules to protein receptors through
physics-based computation remains challenging. Though inroads have been made
using free energy methods, these fail when the underlying classical mechanical
force fields are insufficient. In principle, a more accurate approach is
provided by quantum mechanical density functional theory (DFT) scoring, but
even with approximations, this has yet to become practical on drug
discovery-relevant timescales and resources. Here, we describe how to overcome
this barrier using algorithms for DFT calculations that scale on widely
available cloud architectures, enabling full density functional theory, without
approximations, to be applied to protein-ligand complexes with approximately
2500 atoms in tens of minutes. Applying this to a realistic example of 22
ligands binding to MCL1 reveals that density functional scoring outperforms
classical free energy perturbation theory for this system. This raises the
possibility of broadly applying fully quantum mechanical scoring to real-world
drug discovery pipelines.Comment: 15 pages, 5 figures, 1 tabl
The electrostatic potential profile along a biased molecular wire: A model quantum mechanical calculation
We study the electrostatic potential of a molecular wire bridging two
metallic electrodes in the limit of weak contacts. With the use of a
tight-binding model including a fully three-dimensional treatment of the
electrostatics of the molecular junction, the potential is shown to be poorly
screened, dropping mostly along the entire molecule. In addition, we observe
pronounced Friedel oscillations that can be related to the breaking of
electron-hole symmetry. Our results are in semi-quantitative agreement with
recent state-of-the-art ab initio calculations and point to the need of a
three-dimensional treatment to properly capture the behavior of the
electrostatic potential. Based on these results, current-voltage curves are
calculated within the Landauer formalism. It is shown that Coulomb interaction
partially compensates the localization of the charges induced by the electric
field and consequently tends to suppress zones of negative differential
resistance.Comment: 8 pages, 5 figures, RevTeX
- …