Related papers: Embedding protein 3D-structures in a cubic lattice…

Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…

Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…

We prove identities generating higher dimensional vector partitions. We derive theorems for integer lattice points in the 2D first quadrant, then generalize the approach to find 3D and $n$-space lattice point vector region extensions. We…

The task of programming a quantum computer is just as strange as quantum mechanics itself. But it now looks like a simple 3D puzzle may be the future tool of quantum software engineers.

With the soaring demand for high-performing integrated circuits, 3D integrated circuits (ICs) have emerged as a promising alternative to traditional planar structures. Unlike existing 3D ICs that stack 2D layers, a full 3D IC features cubic…

Shaping the electron wavefunction in three dimensions may prove to be an indispensable tool for research involving atomic-sized particle trapping, manipulation, and synthesis. We utilize computer-generated holograms to sculpt electron…

The regular structures obtained by optical lattice technology and their behaviour are analysed from the quantum information perspective. Initially, we demonstrate that a triangular optical lattice of two atomic species, bosonic or…

Complex systems may morph between structures with different dimensionality and degrees of freedom. As a tool for their modelling, nonlinear embeddings are introduced that encompass objects with different dimensionality as a continuous…

The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…

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…

The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…

Current nanostructure fabrication by etching is usually limited to planar structures as they are defined by a planar mask. The realisation of three-dimensional (3D) nanostructures by etching requires technologies beyond planar masks. We…

We present a coherent filtering scheme which dramatically reduces the site occupation number defects for atoms in an optical lattice, by transferring a chosen number of atoms to a different internal state via adiabatic passage. With the…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…

Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first…

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…

A theoretical model of shape-anisometric particles embedded in a cubic lattice is formulated for binary mixtures combining rod-like, plate-like and spherical particles. The model aims at providing a tool for the prediction and…

The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…