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The numerical simulation of granular systems of even moderate size is a challenging computational problem. In most investigations, either Molecular Dynamics or Event-driven Molecular Dynamics is applied. Here we show that in certain cases,…
Atom optics demonstrates optical phenomena with coherent matter waves, providing a foundational connection between light and matter. Significant advances in optics have followed the realisation of structured light fields hosting complex…
Topological surgery occurs in natural phenomena where two points are selected and attracting or repelling forces are applied. The two points are connected via an invisible `thread'. In order to model topologically such phenomena we…
One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching…
The key obstacle to the realization of a scalable quantum computer is overcoming environmental and control errors. Topological quantum computation has attracted great attention because it has emerged as one of the most promising approaches…
A time crystal is a time dependent physical system that does not reach a standstill, even in state of minimum energy. Here we show that the stability of a time crystal can be enhanced by its topology. For this we simulate time crystals made…
We study one-dimensional topological models with dimerization and trimerization and show that these models can be generated using interaction or optical superlattice. The topological properties of these models are demonstrated by the…
We tackle the challenging problem of creating full and accurate three dimensional reconstructions of botanical trees with the topological and geometric accuracy required for subsequent physical simulation, e.g. in response to wind forces.…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
The dipole moment is a physical quantity indicating the polarity of a molecule and is determined by reflecting the electrical properties of constituent atoms and the geometric properties of the molecule. Most embeddings used to represent…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
Streamlines, vortex lines and magnetic flux tubes in turbulent fluids and plasmas display a great amount of coiling, twisting and linking, raising the question as to whether their topological complexity (continually created and destroyed by…
The Voronoi diagrams are an important tool having theoretical and practical applications in a large number of fields. We present a new procedure, implemented as a set of CUDA kernels, which detects, in a general and efficient way,…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum…
Despite high-dimensionality of images, the sets of images of 3D objects have long been hypothesized to form low-dimensional manifolds. What is the nature of such manifolds? How do they differ across objects and object classes? Answering…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…