Related papers: Embedding protein 3D-structures in a cubic lattice…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Developing a packaging scheme that meets all of the requirements for operation of solid-state qubits in a cryogenic environment can be a formidable challenge. In this article, we discuss work being done in our group as well as in the…
Optical lattices serve as fundamental building blocks for atomic quantum technology. However, the scale and resolution of these lattices are diffraction-limited to the light wavelength. In conventional lattices, achieving tight confinement…
Encoding a dimension in the internal degree of freedom of an atom provides an interesting tool for quantum simulation, facilitating the realization of artificial gauge fields. We propose an extension of the synthetic dimension toolbox,…
We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…
We prove that there is a lattice embedded from every countable distributive lattice into the Boolean algebra of computable subsets of $\mathbb{N}$. Along the way, we discuss all relevant results about lattices, Boolean algebras and…
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…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require.…
Partitionings (or segmentations) divide a given domain into disjoint connected regions whose union forms again the entire domain. Multi-dimensional partitionings occur, for example, when analyzing parameter spaces of simulation models,…
Representation learning and \emph{de novo} generation of proteins are pivotal computational biology tasks. Whilst natural language processing (NLP) techniques have proven highly effective for protein sequence modelling, structure modelling…
Many lattice-based crypstosystems employ ideal lattices for high efficiency. However, the additional algebraic structure of ideal lattices usually makes us worry about the security, and it is widely believed that the algebraic structure…
An embedding is a function that maps entities from one algebraic structure into another while preserving certain characteristics. Embeddings are being used successfully for mapping relational data or text into vector spaces where they can…
This work proposes an alternative approach to the so-called lattice of embedded subsets, which is included in the product of the subset and partition lattices of a finite set, and whose elements are pairs consisting of a subset and a…
We present a proposal for quantum information processing with neutral atoms trapped in optical lattices as qubits. Initialization and coherent control of single qubits can be achieved with standard laser cooling and spectroscopic…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
In this paper we introduce a new class of integrable 3D lattice models, possessing continuous families of commuting layer-to-layer transfer matrices. Algebraically, this commutativity is based on a very special construction of local…
The simple cubic lattice defines a set of points at regular distances. The volume of the Voronoi cells around each point may serve as a weight for integration over the entire space. We add interstitial points to this grid according to the…
We simulated the Coulomb explosion dynamics due to the fast ionization induced by high-intensity X-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual…