Related papers: Quantum Proteomics
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
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…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
With rapid progress being made in the development of platforms for quantum computation, there has been considerable interest in whether present-day and near-term devices can be used to solve problems of relevance. A commonly cited…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…
The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of…
Quantum thermodynamics has emerged as a central field for understanding how energy conversion processes occur in microscopic systems. In these systems, effects such as coherence, entanglement, and non-Markovianity play key roles. In this…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Microscopically probing quantum many-body systems by resolving their constituent particles is essential for understanding quantum matter. In most physical systems, distinguishing individual particles, such as electrons in solids, or…
We investigate the problem of signal transduction via a descriptive analysis of the spatial organization of the complement of proteins exerting a certain function within a cellular compartment. We propose a scheme to assign a numerical…
This review is devoted to precision physics of simple atoms. The atoms can essentially be described in the framework of quantum electrodynamics (QED), however, the energy levels are also affected by the effects of the strong interaction due…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
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…
Machine learning is a fascinating and exciting field within computer science. Recently, this excitement has been transferred to the quantum information realm. Currently, all proposals for the quantum version of machine learning utilize the…
Despite the recent advancements by deep learning methods such as AlphaFold2, \textit{in silico} protein structure prediction remains a challenging problem in biomedical research. With the rapid evolution of quantum computing, it is natural…
We examine the quantum coherence properties of tubulin heterodimers arranged into the protofilaments of cytoskeletal microtubules. In the physical model proposed by the authors, the microtubule interiors are treated as high-Q quantum…
Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous inclusion and prediction of protein backbone and sidechain structure information.…