Related papers: Knot Visualization Experiments for Verifiable Mole…
Vascular networks play a crucial role in understanding brain functionalities. Brain integrity and function, neuronal activity and plasticity, which are crucial for learning, are actively modulated by their local environments, specifically…
We introduce a protocol for the fast simulation of $n$-dimensional quantum systems on $n$-qubit quantum computers with tunable couplings. A mapping is given between the control parameters of the quantum computer and the matrix elements of…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
Understanding the topological characteristics of data is important to many areas of research. Recent work has demonstrated that synthetic 4D image-type data can be useful to train 4D convolutional neural network models to see topological…
We use molecular dynamics to study the ordering of a nematic liquid crystal around a spherical particle or droplet. Homeotropic boundary conditions and strong anchoring create a hedgehog director configuration on the particle surface and in…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Seeking effective neural networks is a critical and practical field in deep learning. Besides designing the depth, type of convolution, normalization, and nonlinearities, the topological connectivity of neural networks is also important.…
Topological data analysis (TDA) detects geometric structure in biological data. However, many TDA algorithms are memory intensive and impractical for massive datasets. Here, we introduce a statistical protocol that reduces TDA's memory…
Two-dimensional simulations are used to explore topological transitions that occur during the formation of films grown from grains that are seeded on substrates. This is done for a relatively large range of the initial value $\Phi_s$ of the…
The results of numerical simulation of the interaction of topological solitons (2+1)-dimensional O(3) non-linear sigma model in reversed time are presented. At the first stage, models of interactions of topological vortices are developed,…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Coordination geometries describe how the neighbours of a central particle are arranged around it. Such geometries can be thought to lie in an abstract topological space; a model of this space could provide a mathematical basis for…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
In the field of quantum simulation of condensed matter phenomena by artificially engineering the Hamiltonian of an atomic, molecular or optical system, the concept of `synthetic dimensions' has recently emerged as a powerful way to emulate…
Generating precise 3D molecular geometries is crucial for drug discovery and material science. While prior efforts leverage 1D representations like SELFIES to ensure molecular validity, they fail to fully exploit the rich chemical knowledge…
In the last decades cosmological N-body dark matter simulations have enabled ab initio studies of the formation of structure in the Universe. Gravity amplified small density fluctuations generated shortly after the Big Bang, leading to the…
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend…
Quantum computers hold promise to enable efficient simulations of the properties of molecules and materials; however, at present they only permit ab initio calculations of a few atoms, due to a limited number of qubits. In order to harness…