Related papers: Knot Visualization Experiments for Verifiable Mole…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The chiral soliton lattice is an array of topological solitons realized as ground states of QCD at finite density under strong magnetic fields or rapid rotation, and chiral magnets with an easy-plane anisotropy. In such cases, topological…
Artificial neural networks and machine learning have now reached a new era after several decades of improvement where applications are to explode in many fields of science, industry, and technology. Here, we use artificial neural networks…
Bounding volumes are an established concept in computer graphics and vision tasks but have seen little change since their early inception. In this work, we study the use of neural networks as bounding volumes. Our key observation is that…
Quantum-information-inspired experiments in nuclear magnetic resonance spectroscopy may yield a pathway towards determining molecular structure and properties that are otherwise challenging to learn. We measure out-of-time-ordered…
We use the nudged elastic band method from computational chemistry to analyze high-dimensional data. Our approach is inspired by Morse theory, and as output we produce an increasing sequence of small cell complexes modeling the dense…
Topological techniques are used to study the motions of systems of point vortices in the infinite plane, in singly-periodic arrays, and in doubly-periodic lattices. The reduction of each system using its symmetries is described in detail.…
Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Three-dimensional particle tracking velocimetry (3D-PTV) technique is widely used to acquire the complicated trajectories of particles and flow fields. It is known that the accuracy of 3D-PTV depends on the mapping function to reconstruct…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based…
Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…
Shallow flow or thin liquid film models are used for a wide range of physical and engineering problems. Shallow flow models allow capturing the free surface of the fluid with little effort and reducing the three-dimensional problem to a…
Rigid body interactions are fundamental to numerous scientific disciplines, but remain challenging to simulate due to their abrupt nonlinear nature and sensitivity to complex, often unknown environmental factors. These challenges call for…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship…
Segmentation is often an essential intermediate step in image analysis. A volume segmentation characterizes the underlying volume image in terms of geometric information--segments, faces between segments, curves in which several faces…
We present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…