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Non-equilibrium assembly, driven by fluxes controllable by continuous external energy inputs, enables dynamic and reconfigurable structures. Such controlled 3D assembly is desired for the design of adaptive materials that exploit…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
Metal-organic frameworks (MOFs) marry inorganic nodes, organic edges, and topological nets into programmable porous crystals, yet their astronomical design space defies brute-force synthesis. Generative modeling holds ultimate promise, but…
The coupled evolution of the magnetic field and the flow at the Earth's core mantle boundary is modeled within the 1900.0-2014.0 time period. To constraint the dynamical behavior of the system with a core field model deriving from direct…
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…
A hybrid spectral/finite-element code is developed to numerically solve the resistive finite-pressure magnetohydrodynamic equilibria without the necessity of postulating nested magnetic flux surfaces in the non-axisymmetric toroidal…
Graph neural networks (GNNs) have achieved remarkable success in molecular property prediction. However, traditional graph representations struggle to effectively encode the inherent 3D spatial structures of molecules, as molecular…
The three-dimensional evolution of a pure electron plasma is studied by means of a particle-in-cell code which solves the drift-Poisson system where kinetic effects in the motion parallel to the magnetic field are taken into account.…
In this article, the electronic band structure $\beta-(Al_xGa_{1-x})_2O_3$ alloy system is calculated with $\beta-Ga_2O_3$ as the bulk crystal. The technique of band unfolding is implemented to obtain the effective bandstructure…
We describe extensions to the siesta density functional theory (dft) code [30], for the simulation of isolated molecules and their absorption spectra. The extensions allow for: - Use of a multi-grid solver for the Poisson equation on a…
The applicability of the highly idealized secondary infall model to `realistic' initial conditions is investigated. The collapse of proto-halos seeded by $3\sigma$ density perturbations to an Einstein--de Sitter universe is studied here for…
A paradigm proposed recently by Boal et al. (A.K. Boal et al., Nature 404, 746-748, 2000) deals with the possibility to use inorganic nanoparticles as building blocks for the design and fabrication of colloidal and supracolloidal…
In this paper, we propose to enhance the performance of the sum-product algorithm (SPA) by interleaving SPA iterations with a random local graph update rule. This rule is known as edge local complementation (ELC), and has the effect of…
A process-theoretic approach to electrodynamics based on persistent Kac-type stochastic processes is developed. Finite-velocity stochastic propagation is taken as primary, while relativistic wave equations arise as emergent descriptions…
Multi-view echocardiographic sequences segmentation is crucial for clinical diagnosis. However, this task is challenging due to limited labeled data, huge noise, and large gaps across views. Here we propose a recurrent aggregation learning…
This paper proposes an optimization-based framework for the analysis of multiperiod directed multihypergraphs aimed at identifying self-amplifying structures that sustain endogenous growth in complex systems. The approach captures the…
We report a multiscale approach of broad applicability to stochastic reconstruction of multiphase materials, including porous ones. The approach devised uses an optimization method, such as the simulated annealing (SA) and the so-called…
One of the main diagnostic tools for measuring electron density profiles and the characteristics of long wavelength turbulent wave structures in fusion plasmas is Beam Emission Spectroscopy (BES). The increasing number of BES systems…
Dynamics of flexible ferromagnetic filaments in an external magnetic field is considered. We report the existence of a buckling instability of the ferromagnetic filament at the magnetic field reversion, which leads to the formation of a…