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We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e. fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the Root Mean Square Distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e. their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.
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Interpreting molecular dynamics simulations usually involves automated classification of local atomic environments to identify regions of interest. Existing approaches are generally limited to a small number of reference structures and only include limited information about the local chemical composition. This work proposes to use a variant of the Gromov-Wasserstein (GW) distance to quantify the difference between a local atomic environment and a set of arbitrary reference environments in a way that is sensitive to atomic displacements, missing atoms, and differences in chemical composition. This involves describing a local atomic environment as a finite metric measure space, which has the additional advantages of not requiring the local environment to be centered on an atom and of not making any assumptions about the material class. Numerical examples illustrate the efficacy and versatility of the algorithm.
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Permutation invariant Gaussian matrix models were recently developed for applications in computational linguistics. A 5-parameter family of models was solved. In this paper, we use a representation theoretic approach to solve the general 13-parameter Gaussian model, which can be viewed as a zero-dimensional quantum field theory. We express the two linear and eleven quadratic terms in the action in terms of representation theoretic parameters. These parameters are coefficients of simple quadratic expressions in terms of appropriate linear combinations of the matrix variables transforming in specific irreducible representations of the symmetric group $S_D$ where $D$ is the size of the matrices. They allow the identification of constraints which ensure a convergent Gaussian measure and well-defined expectation values for polynomial functions of the random matrix at all orders. A graph-theoretic interpretation is known to allow the enumeration of permutation invariants of matrices at linear, quadratic and higher orders. We express the expectation values of all the quadratic graph-basis invariants and a selection of cubic and quartic invariants in terms of the representation theoretic parameters of the model.
We have studied the effect of thermal effects on the structural and transport response of Ag atomic-size nanowires generated by mechanical elongation. Our study involves both time-resolved atomic resolution transmission electron microscopy imaging and quantum conductance measurement using an ultra-high-vacuum mechanically controllable break junction. We have observed drastic changes in conductance and structural properties of Ag nanowires generated at different temperatures (150 and 300 K). By combining electron microscopy images, electronic transport measurements and quantum transport calculations, we have been able to obtain a consistent correlation between the conductance and structural properties of Ag NWs. In particular, our study has revealed the formation of metastable rectangular rod-like Ag wire (3/3) along the (001) crystallographic direction, whose formation is enhanced. These results illustrate the high complexity of analyzing structural and quantum conductance behaviour of metal atomic-size wires; also, they reveal that it is extremely difficult to compare NW conductance experiments performed at different temperatures due to the fundamental modifications of the mechanical behavior.
In a research context, image acquisition will often involve a pre-defined static protocol and the data will be of high quality. If we are to build applications that work in hospitals without significant operational changes in care delivery, algorithms should be designed to cope with the available data in the best possible way. In a clinical environment, imaging protocols are highly flexible, with MRI sequences commonly missing appropriate sequence labeling (e.g. T1, T2, FLAIR). To this end we introduce PIMMS, a Permutation Invariant Multi-Modal Segmentation technique that is able to perform inference over sets of MRI scans without using modality labels. We present results which show that our convolutional neural network can, in some settings, outperform a baseline model which utilizes modality labels, and achieve comparable performance otherwise.
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