603 research outputs found
Non-Adiabatic Potential-Energy Surfaces by Constrained Density-Functional Theory
Non-adiabatic effects play an important role in many chemical processes. In
order to study the underlying non-adiabatic potential-energy surfaces (PESs),
we present a locally-constrained density-functional theory approach, which
enables us to confine electrons to sub-spaces of the Hilbert space, e.g. to
selected atoms or groups of atoms. This allows to calculate non-adiabatic PESs
for defined charge and spin states of the chosen subsystems. The capability of
the method is demonstrated by calculating non-adiabatic PESs for the scattering
of a sodium and a chlorine atom, for the interaction of a chlorine molecule
with a small metal cluster, and for the dissociation of an oxygen molecule at
the Al(111) surface.Comment: 11 pages including 7 figures; related publications can be found at
http://www.fhi-berlin.mpg.de/th/th.htm
Nucleation mechanism for the direct graphite-to-diamond phase transition
Graphite and diamond have comparable free energies, yet forming diamond from
graphite is far from easy. In the absence of a catalyst, pressures that are
significantly higher than the equilibrium coexistence pressures are required to
induce the graphite-to-diamond transition. Furthermore, the formation of the
metastable hexagonal polymorph of diamond instead of the more stable cubic
diamond is favored at lower temperatures. The concerted mechanism suggested in
previous theoretical studies cannot explain these phenomena. Using an ab initio
quality neural-network potential we performed a large-scale study of the
graphite-to-diamond transition assuming that it occurs via nucleation. The
nucleation mechanism accounts for the observed phenomenology and reveals its
microscopic origins. We demonstrated that the large lattice distortions that
accompany the formation of the diamond nuclei inhibit the phase transition at
low pressure and direct it towards the hexagonal diamond phase at higher
pressure. The nucleation mechanism proposed in this work is an important step
towards a better understanding of structural transformations in a wide range of
complex systems such as amorphous carbon and carbon nanomaterials
Deja Vu: semantics-aware recording and replay of high-speed eye tracking and interaction data to support cognitive studies of software engineering tasks—methodology and analyses
The paper introduces a fundamental technological problem with collecting high-speed eye tracking data while studying software engineering tasks in an integrated development environment. The use of eye trackers is quickly becoming an important means to study software developers and how they comprehend source code and locate bugs. High quality eye trackers can record upwards of 120 to 300 gaze points per second. However, it is not always possible to map each of these points to a line and column position in a source code file (in the presence of scrolling and file switching) in real time at data rates over 60 gaze points per second without data loss. Unfortunately, higher data rates are more desirable as they allow for finer granularity and more accurate study analyses. To alleviate this technological problem, a novel method for eye tracking data collection is presented. Instead of performing gaze analysis in real time, all telemetry (keystrokes, mouse movements, and eye tracker output) data during a study is recorded as it happens. Sessions are then replayed at a much slower speed allowing for ample time to map gaze point positions to the appropriate file, line, and column to perform additional analysis. A description of the method and corresponding tool, Deja Vu, is presented. An evaluation of the method and tool is conducted using three different eye trackers running at four different speeds (60 Hz, 120 Hz, 150 Hz, and 300 Hz). This timing evaluation is performed in Visual Studio, Eclipse, and Atom IDEs. Results show that Deja Vu can playback 100% of the data recordings, correctly mapping the gaze to corresponding elements, making it a well-founded and suitable post processing step for future eye tracking studies in software engineering. Finally, a proof of concept replication analysis of four tasks from two previous studies is performed. Due to using the Deja Vu approach, this replication resulted in richer collected data and improved on the number of distinct syntactic categories that gaze was mapped on in the code
Coulomb Gap and Correlated Vortex Pinning in Superconductors
The positions of columnar pins and magnetic flux lines determined from a
decoration experiment on BSCCO were used to calculate the single--particle
density of states at low temperatures in the Bose glass phase. A wide Coulomb
gap is found, with gap exponent , as a result of the long--range
interaction between the vortices. As a consequence, the variable--range hopping
transport of flux lines is considerably reduced with respect to the
non--interacting case, the effective Mott exponent being enhanced from to for this specific experiment.Comment: 10 pages, Revtex, 4 figures appended as uu-encoded postscript files,
also available as hardcopies from [email protected]
Building nonparametric -body force fields using Gaussian process regression
Constructing a classical potential suited to simulate a given atomic system
is a remarkably difficult task. This chapter presents a framework under which
this problem can be tackled, based on the Bayesian construction of
nonparametric force fields of a given order using Gaussian process (GP) priors.
The formalism of GP regression is first reviewed, particularly in relation to
its application in learning local atomic energies and forces. For accurate
regression it is fundamental to incorporate prior knowledge into the GP kernel
function. To this end, this chapter details how properties of smoothness,
invariance and interaction order of a force field can be encoded into
corresponding kernel properties. A range of kernels is then proposed,
possessing all the required properties and an adjustable parameter
governing the interaction order modelled. The order best suited to describe
a given system can be found automatically within the Bayesian framework by
maximisation of the marginal likelihood. The procedure is first tested on a toy
model of known interaction and later applied to two real materials described at
the DFT level of accuracy. The models automatically selected for the two
materials were found to be in agreement with physical intuition. More in
general, it was found that lower order (simpler) models should be chosen when
the data are not sufficient to resolve more complex interactions. Low GPs
can be further sped up by orders of magnitude by constructing the corresponding
tabulated force field, here named "MFF".Comment: 31 pages, 11 figures, book chapte
Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-<i>cas</i> gene cassettes reveals 39 new <i>cas</i> gene families
Interactions, Distribution of Pinning Energies, and Transport in the Bose Glass Phase of Vortices in Superconductors
We study the ground state and low energy excitations of vortices pinned to
columnar defects in superconductors, taking into account the long--range
interaction between the fluxons. We consider the ``underfilled'' situation in
the Bose glass phase, where each flux line is attached to one of the defects,
while some pins remain unoccupied. By exploiting an analogy with disordered
semiconductors, we calculate the spatial configurations in the ground state, as
well as the distribution of pinning energies, using a zero--temperature Monte
Carlo algorithm minimizing the total energy with respect to all possible
one--vortex transfers. Intervortex repulsion leads to strong correlations
whenever the London penetration depth exceeds the fluxon spacing. A pronounced
peak appears in the static structure factor for low filling fractions . Interactions lead to a broad Coulomb gap in the distribution of
pinning energies near the chemical potential , separating
the occupied and empty pins. The vanishing of at leads to a
considerable reduction of variable--range hopping vortex transport by
correlated flux line pinning.Comment: 16 pages (twocolumn), revtex, 16 figures not appended, please contact
[email protected]
A Comparative Study of Embedded and Anesthetized Zebrafish in vivo on Myocardiac Calcium Oscillation and Heart Muscle Contraction
The zebrafish (Danio rerio) has been used as a model for studying vertebrate development in the cardiovascular system. In order to monitor heart contraction and cytosolic calcium oscillations, fish were either embedded in methylcellulose or anesthetized with tricaine. Using high-resolution differential interference contrast and calcium imaging microscopy, we here show that dopamine and verapamil alter calcium signaling and muscle contraction in anesthetized zebrafish, but not in embedded zebrafish. In anesthetized fish, dopamine increases the amplitude of cytosolic calcium oscillation with a subsequent increase in heart contraction, whereas verapamil decreases the frequency of calcium oscillation and heart rate. Interestingly, verapamil also increases myocardial contraction. Our data further indicate that verapamil can increase myocardial calcium sensitivity in anesthetized fish. Taken together, our data reinforce in vivo cardiac responses to dopamine and verapamil. Furthermore, effects of dopamine and verapamil on myocardial calcium and contraction are greater in anesthetized than embedded fish. We suggest that while the zebrafish is an excellent model for a cardiovascular imaging study, the cardio-pharmacological profiles are very different between anesthetized and embedded fish
Atomic-scale representation and statistical learning of tensorial properties
This chapter discusses the importance of incorporating three-dimensional
symmetries in the context of statistical learning models geared towards the
interpolation of the tensorial properties of atomic-scale structures. We focus
on Gaussian process regression, and in particular on the construction of
structural representations, and the associated kernel functions, that are
endowed with the geometric covariance properties compatible with those of the
learning targets. We summarize the general formulation of such a
symmetry-adapted Gaussian process regression model, and how it can be
implemented based on a scheme that generalizes the popular smooth overlap of
atomic positions representation. We give examples of the performance of this
framework when learning the polarizability and the ground-state electron
density of a molecule
Machine-learning of atomic-scale properties based on physical principles
We briefly summarize the kernel regression approach, as used recently in
materials modelling, to fitting functions, particularly potential energy
surfaces, and highlight how the linear algebra framework can be used to both
predict and train from linear functionals of the potential energy, such as the
total energy and atomic forces. We then give a detailed account of the Smooth
Overlap of Atomic Positions (SOAP) representation and kernel, showing how it
arises from an abstract representation of smooth atomic densities, and how it
is related to several popular density-based representations of atomic
structure. We also discuss recent generalisations that allow fine control of
correlations between different atomic species, prediction and fitting of
tensorial properties, and also how to construct structural kernels---applicable
to comparing entire molecules or periodic systems---that go beyond an additive
combination of local environments
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