12,175 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
Towards electron transport measurements in chemically modified graphene: The effect of a solvent
Chemical functionalization of graphene modifies the local electron density of
the carbon atoms and hence electron transport. Measuring these changes allows
for a closer understanding of the chemical interaction and the influence of
functionalization on the graphene lattice. However, not only chemistry, in this
case diazonium chemistry, has an effect on the electron transport. Latter is
also influenced by defects and dopants resulting from different processing
steps. Here, we show that solvents used in the chemical reaction process change
the transport properties. In more detail, the investigated combination of
isopropanol and heating treatment reduces the doping concentration and
significantly increases the mobility of graphene. Furthermore, the isopropanol
treatment alone increases the concentration of dopants and introduces an
asymmetry between electron and hole transport which might be difficult to
distinguish from the effect of functionalization. The results shown in this
work demand a closer look on the influence of solvents used for chemical
modification in order to understand their influence
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
Secondary Structures in Long Compact Polymers
Compact polymers are self-avoiding random walks which visit every site on a
lattice. This polymer model is used widely for studying statistical problems
inspired by protein folding. One difficulty with using compact polymers to
perform numerical calculations is generating a sufficiently large number of
randomly sampled configurations. We present a Monte-Carlo algorithm which
uniformly samples compact polymer configurations in an efficient manner
allowing investigations of chains much longer than previously studied. Chain
configurations generated by the algorithm are used to compute statistics of
secondary structures in compact polymers. We determine the fraction of monomers
participating in secondary structures, and show that it is self averaging in
the long chain limit and strictly less than one. Comparison with results for
lattice models of open polymer chains shows that compact chains are
significantly more likely to form secondary structure.Comment: 14 pages, 14 figure
Graphene on metals: a Van der Waals density functional study
We use density functional theory (DFT) with a recently developed van der
Waals density functional (vdW-DF) to study the adsorption of graphene on Al,
Cu, Ag, Au, Pt, Pd, Co and Ni(111) surfaces. In constrast to the local density
approximation (LDA) which predicts relatively strong binding for Ni,Co and Pd,
the vdW-DF predicts weak binding for all metals and metal-graphene distances in
the range 3.40-3.72 \AA. At these distances the graphene bandstructure as
calculated with DFT and the many-body GW method is basically unaffected
by the substrate, in particular there is no opening of a band gap at the
-point.Comment: 4 pages, 3 figure
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
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
Advanced tracking systems design and analysis
The results of an assessment of several types of high-accuracy tracking systems proposed to track the spacecraft in the National Aeronautics and Space Administration (NASA) Advanced Tracking and Data Relay Satellite System (ATDRSS) are summarized. Tracking systems based on the use of interferometry and ranging are investigated. For each system, the top-level system design and operations concept are provided. A comparative system assessment is presented in terms of orbit determination performance, ATDRSS impacts, life-cycle cost, and technological risk
Graphene Rings in Magnetic Fields: Aharonov-Bohm Effect and Valley Splitting
We study the conductance of mesoscopic graphene rings in the presence of a
perpendicular magnetic field by means of numerical calculations based on a
tight-binding model. First, we consider the magnetoconductance of such rings
and observe the Aharonov-Bohm effect. We investigate different regimes of the
magnetic flux up to the quantum Hall regime, where the Aharonov-Bohm
oscillations are suppressed. Results for both clean (ballistic) and disordered
(diffusive) rings are presented. Second, we study rings with smooth mass
boundary that are weakly coupled to leads. We show that the valley degeneracy
of the eigenstates in closed graphene rings can be lifted by a small magnetic
flux, and that this lifting can be observed in the transport properties of the
system.Comment: 12 pages, 9 figure
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