548 research outputs found
Rigidity of Orientationally Ordered Domains of Short Chain Molecules
By molecular dynamics simulation, discovered is a strange rigid-like nature
for a hexagonally packed domain of short chain molecules. In spite of the
non-bonded short-range interaction potential (Lennard-Jones potential) among
chain molecules, the packed domain gives rise to a resultant global moment of
inertia. Accordingly, as two domains encounter obliquely, they rotate so as to
be parallel to each other keeping their overall structures as if they were
rigid bodies.Comment: 7 pages, 5 figures, and 2 table
Algorithm for numerical integration of the rigid-body equations of motion
A new algorithm for numerical integration of the rigid-body equations of
motion is proposed. The algorithm uses the leapfrog scheme and the quantities
involved are angular velocities and orientational variables which can be
expressed in terms of either principal axes or quaternions. Due to specific
features of the algorithm, orthonormality and unit norms of the orientational
variables are integrals of motion, despite an approximate character of the
produced trajectories. It is shown that the method presented appears to be the
most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur
Atomistic mechanisms for the ordered growth of Co nano-dots on Au(788): comparison of VT-STM experiments and multi-scaled calculations
Hetero-epitaxial growth on a strain-relief vicinal patterned substrate has
revealed unprecedented 2D long range ordered growth of uniform cobalt
nanostructures. The morphology of a Co sub-monolayer deposit on a Au(111)
reconstructed vicinal surface is analyzed by Variable Temperature Scanning
Tunneling Microscopy (VT-STM) experiments. A rectangular array of nano-dots
(3.8 nm x 7.2 nm) is found for a particularly large deposit temperature range
lying from 60 K to 300 K. Although the nanodot lattice is stable at room
temperature, this paper focus on the early stage of ordered nucleation and
growth at temperatures between 35 K and 480 K. The atomistic mechanisms leading
to the nanodots array are elucidated by comparing statistical analysis of
VT-STM images with multi-scaled numerical calculations combining both Molecular
Dynamics for the quantitative determination of the activation energies for the
atomic motion and the Kinetic Monte Carlo method for the simulations of the
mesoscopic time and scale evolution of the Co submonolayer
Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma
Classical Molecular Dynamics (MD) simulations for a one-component plasma
(OCP) are presented. Quantum effects are included in the form of the Kelbg
potential. Results for the dynamical structure factor are compared with the
Vlasov and RPA (random phase approximation) theories. The influence of the
coupling parameter , degeneracy parameter and the form
of the pair interaction on the optical plasmon dispersion is investigated. An
improved analytical approximation for the dispersion of Langmuir waves is
presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table
Discovery of Bright Galactic R Coronae Borealis and DY Persei Variables: Rare Gems Mined from ACVS
We present the results of a machine-learning (ML) based search for new R
Coronae Borealis (RCB) stars and DY Persei-like stars (DYPers) in the Galaxy
using cataloged light curves from the All-Sky Automated Survey (ASAS) Catalog
of Variable Stars (ACVS). RCB stars - a rare class of hydrogen-deficient
carbon-rich supergiants - are of great interest owing to the insights they can
provide on the late stages of stellar evolution. DYPers are possibly the
low-temperature, low-luminosity analogs to the RCB phenomenon, though
additional examples are needed to fully establish this connection. While RCB
stars and DYPers are traditionally identified by epochs of extreme dimming that
occur without regularity, the ML search framework more fully captures the
richness and diversity of their photometric behavior. We demonstrate that our
ML method can use newly discovered RCB stars to identify additional candidates
within the same data set. Our search yields 15 candidates that we consider
likely RCB stars/DYPers: new spectroscopic observations confirm that four of
these candidates are RCB stars and four are DYPers. Our discovery of four new
DYPers increases the number of known Galactic DYPers from two to six;
noteworthy is that one of the new DYPers has a measured parallax and is m ~ 7
mag, making it the brightest known DYPer to date. Future observations of these
new DYPers should prove instrumental in establishing the RCB connection. We
consider these results, derived from a machine-learned probabilistic
classification catalog, as an important proof-of-concept for the efficient
discovery of rare sources with time-domain surveys.Comment: 18 pages, 2 new figures, accepted for publication in Ap
Elaborating Transition Interface Sampling Methods
We review two recently developed efficient methods for calculating rate
constants of processes dominated by rare events in high-dimensional complex
systems. The first is transition interface sampling (TIS), based on the
measurement of effective fluxes through hypersurfaces in phase space. TIS
improves efficiency with respect to standard transition path sampling (TPS)
rate constant techniques, because it allows a variable path length and is less
sensitive to recrossings. The second method is the partial path version of TIS.
Developed for diffusive processes, it exploits the loss of long time
correlation. We discuss the relation between the new techniques and the
standard reactive flux methods in detail. Path sampling algorithms can suffer
from ergodicity problems, and we introduce several new techniques to alleviate
these problems, notably path swapping, stochastic configurational bias Monte
Carlo shooting moves and order-parameter free path sampling. In addition, we
give algorithms to calculate other interesting properties from path ensembles
besides rate constants, such as activation energies and reaction mechanisms.Comment: 36 pages, 5 figure
The Dutchman Vol. 6, No. 1
● Editorial ● Somerset County Decorated Barns ● Butter Molds ● Restaurants, too, Go Dutch ● The Hostetter Fractur Collection ● Bindnagle\u27s Church ● The Harry S. High Folk Art Collection ● Lebanon Valley Date Stones ● Of Bells and Bell Towers ● John Durang, the First Native American Dancer ● Stoffel Rilbps\u27 Epistle ● The First Singing of Our National Anthem ● Pennsylvania Dutch Pioneershttps://digitalcommons.ursinus.edu/dutchmanmag/1000/thumbnail.jp
Atomic-scale modeling of the deformation of nanocrystalline metals
Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display
technologically interesting properties, such as dramatically increased
hardness, increasing with decreasing grain size. Due to the small grain size,
direct atomic-scale simulations of plastic deformation of these materials are
possible, as such a polycrystalline system can be modeled with the
computational resources available today.
We present molecular dynamics simulations of nanocrystalline copper with
grain sizes up to 13 nm. Two different deformation mechanisms are active, one
is deformation through the motion of dislocations, the other is sliding in the
grain boundaries. At the grain sizes studied here the latter dominates, leading
to a softening as the grain size is reduced. This implies that there is an
``optimal'' grain size, where the hardness is maximal.
Since the grain boundaries participate actively in the deformation, it is
interesting to study the effects of introducing impurity atoms in the grain
boundaries. We study how silver atoms in the grain boundaries influence the
mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in
Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see
http://www.fysik.dtu.dk/~schiotz/publist.htm
Spontaneous alloying in binary metal microclusters - A molecular dynamics study -
Microcanonical molecular dynamics study of the spontaneous alloying(SA),
which is a manifestation of fast atomic diffusion in a nano-sized metal
cluster, is done in terms of a simple two dimensional binary Morse model.
Important features observed by Yasuda and Mori are well reproduced in our
simulation. The temperature dependence and size dependence of the SA phenomena
are extensively explored by examining long time dynamics. The dominant role of
negative heat of solution in completing the SA is also discussed. We point out
that a presence of melting surface induces the diffusion of core atoms even if
they are solid-like. In other words, the {\it surface melting} at substantially
low temperature plays a key role in attaining the SA.Comment: 15 pages, 12 fgures, Submitted to Phys.Rev.
Exploring the Free Energy Landscape: From Dynamics to Networks and Back
The knowledge of the Free Energy Landscape topology is the essential key to
understand many biochemical processes. The determination of the conformers of a
protein and their basins of attraction takes a central role for studying
molecular isomerization reactions. In this work, we present a novel framework
to unveil the features of a Free Energy Landscape answering questions such as
how many meta-stable conformers are, how the hierarchical relationship among
them is, or what the structure and kinetics of the transition paths are.
Exploring the landscape by molecular dynamics simulations, the microscopic data
of the trajectory are encoded into a Conformational Markov Network. The
structure of this graph reveals the regions of the conformational space
corresponding to the basins of attraction. In addition, handling the
Conformational Markov Network, relevant kinetic magnitudes as dwell times or
rate constants, and the hierarchical relationship among basins, complete the
global picture of the landscape. We show the power of the analysis studying a
toy model of a funnel-like potential and computing efficiently the conformers
of a short peptide, the dialanine, paving the way to a systematic study of the
Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press
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