10,549 research outputs found
Unbiased sampling of globular lattice proteins in three dimensions
We present a Monte Carlo method that allows efficient and unbiased sampling
of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit
each lattice site exactly once. They are often used as simple models of
globular proteins, upon adding suitable local interactions. Our algorithm can
easily be equipped with such interactions, but we study here mainly the
flexible homopolymer case where each conformation is generated with uniform
probability. We argue that the algorithm is ergodic and has dynamical exponent
z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers.
Results are presented for the effective interaction between end points, and the
interaction with the boundaries of the system
Rate theory for correlated processes: Double-jumps in adatom diffusion
We study the rate of activated motion over multiple barriers, in particular
the correlated double-jump of an adatom diffusing on a missing-row
reconstructed Platinum (110) surface. We develop a Transition Path Theory,
showing that the activation energy is given by the minimum-energy trajectory
which succeeds in the double-jump. We explicitly calculate this trajectory
within an effective-medium molecular dynamics simulation. A cusp in the
acceptance region leads to a sqrt{T} prefactor for the activated rate of
double-jumps. Theory and numerical results agree
Dynamic rotor mode in antiferromagnetic nanoparticles
We present experimental, numerical, and theoretical evidence for a new mode
of antiferromagnetic dynamics in nanoparticles. Elastic neutron scattering
experiments on 8 nm particles of hematite display a loss of diffraction
intensity with temperature, the intensity vanishing around 150 K. However, the
signal from inelastic neutron scattering remains above that temperature,
indicating a magnetic system in constant motion. In addition, the precession
frequency of the inelastic magnetic signal shows an increase above 100 K.
Numerical Langevin simulations of spin dynamics reproduce all measured neutron
data and reveal that thermally activated spin canting gives rise to a new type
of coherent magnetic precession mode. This "rotor" mode can be seen as a
high-temperature version of superparamagnetism and is driven by exchange
interactions between the two magnetic sublattices. The frequency of the rotor
mode behaves in fair agreement with a simple analytical model, based on a high
temperature approximation of the generally accepted Hamiltonian of the system.
The extracted model parameters, as the magnetic interaction and the axial
anisotropy, are in excellent agreement with results from Mossbauer
spectroscopy
Exact enumeration of Hamiltonian circuits, walks, and chains in two and three dimensions
We present an algorithm for enumerating exactly the number of Hamiltonian
chains on regular lattices in low dimensions. By definition, these are sets of
k disjoint paths whose union visits each lattice vertex exactly once. The
well-known Hamiltonian circuits and walks appear as the special cases k=0 and
k=1 respectively. In two dimensions, we enumerate chains on L x L square
lattices up to L=12, walks up to L=17, and circuits up to L=20. Some results
for three dimensions are also given. Using our data we extract several
quantities of physical interest
Monte Carlo Study of Short-Range Order and Displacement Effects in Disordered CuAu
The correlation between local chemical environment and atomic displacements
in disordered CuAu alloy has been studied using Monte Carlo simulations based
on the effective medium theory (EMT) of metallic cohesion. These simulations
correctly reproduce the chemically-specific nearest-neighbor distances in the
random alloy across the entire Cu\$_x\$Au\$_{1-x}\$ concentration range. In the
random equiatomic CuAu alloy, the chemically specific pair distances depend
strongly on the local atomic environment (i.e. fraction of like/unlike nearest
neighbors). In CuAu alloy with short-range order, the relationship between
local environment and displacements remains qualitatively similar. However the
increase in short-range order causes the average Cu-Au distance to decrease
below the average Cu-Cu distance, as it does in the ordered CuAuI phase. Many
of these trends can be understood qualitatively from the different neutral
sphere radii and compressibilities of the Cu and Au atoms.Comment: 9 pages, 5 figures, 2 table
Bayesian Error Estimation in Density Functional Theory
We present a practical scheme for performing error estimates for Density
Functional Theory calculations. The approach which is based on ideas from
Bayesian statistics involves creating an ensemble of exchange-correlation
functionals by comparing with an experimental database of binding energies for
molecules and solids. Fluctuations within the ensemble can then be used to
estimate errors relative to experiment on calculated quantities like binding
energies, bond lengths, and vibrational frequencies. It is demonstrated that
the error bars on energy differences may vary by orders of magnitude for
different systems in good agreement with existing experience.Comment: 5 pages, 3 figure
Computational Design of Chemical Nanosensors: Metal Doped Carbon Nanotubes
We use computational screening to systematically investigate the use of
transition metal doped carbon nanotubes for chemical gas sensing. For a set of
relevant target molecules (CO, NH3, H2S) and the main components of air (N2,
O2, H2O), we calculate the binding energy and change in conductance upon
adsorption on a metal atom occupying a vacancy of a (6,6) carbon nanotube.
Based on these descriptors, we identify the most promising dopant candidates
for detection of a given target molecule. From the fractional coverage of the
metal sites in thermal equilibrium with air, we estimate the change in the
nanotube resistance per doping site as a function of the target molecule
concentration assuming charge transport in the diffusive regime. Our analysis
points to Ni-doped nanotubes as candidates for CO sensors working under typical
atmospheric conditions
Simulations of energetic beam deposition: from picoseconds to seconds
We present a new method for simulating crystal growth by energetic beam
deposition. The method combines a Kinetic Monte-Carlo simulation for the
thermal surface diffusion with a small scale molecular dynamics simulation of
every single deposition event. We have implemented the method using the
effective medium theory as a model potential for the atomic interactions, and
present simulations for Ag/Ag(111) and Pt/Pt(111) for incoming energies up to
35 eV. The method is capable of following the growth of several monolayers at
realistic growth rates of 1 monolayer per second, correctly accounting for both
energy-induced atomic mobility and thermal surface diffusion. We find that the
energy influences island and step densities and can induce layer-by-layer
growth. We find an optimal energy for layer-by-layer growth (25 eV for Ag),
which correlates with where the net impact-induced downward interlayer
transport is at a maximum. A high step density is needed for energy induced
layer-by-layer growth, hence the effect dies away at increased temperatures,
where thermal surface diffusion reduces the step density. As part of the
development of the method, we present molecular dynamics simulations of single
atom-surface collisions on flat parts of the surface and near straight steps,
we identify microscopic mechanisms by which the energy influences the growth,
and we discuss the nature of the energy-induced atomic mobility
Dislocation Kinks in Copper: Widths, Barriers, Effective Masses, and Quantum Tunneling
We calculate the widths, migration barriers, effective masses, and quantum
tunneling rates of kinks and jogs in extended screw dislocations in copper,
using an effective medium theory interatomic potential. The energy barriers and
effective masses for moving a unit jog one lattice constant are close to
typical atomic energies and masses: tunneling will be rare. The energy barriers
and effective masses for the motion of kinks are unexpectedly small due to the
spreading of the kinks over a large number of atoms. The effective masses of
the kinks are so small that quantum fluctuations will be important. We discuss
implications for quantum creep, kink--based tunneling centers, and Kondo
resonances
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