Related papers: Quantum Proteomics
Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…
The mathematical content of the interaction term of quantum electrodynamics is examined under the following assumption: It is presumed that the apparent degrees-of-freedom of the photon field reflect the kinematical degrees-of-freedom of…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
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…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
We explore the potential application of quantum annealing to address the protein structure problem. To this end, we compare several proposed ab initio protein folding models for quantum computers and analyze their scaling and performance…
We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period, in spite of the presence of the interactions with environmental modes of molecular vibration. The…
Quantum Nanomechanics is the emerging field which pertains to the mechanical behavior of nanoscale systems in the quantum domain. Unlike the conventional studies of vibration of molecules and phonons in solids, quantum nanomechanics is…
Searches for the permanent electric dipole moments (EDMs) of molecules, atoms, nucleons and nuclei provide powerful probes of CP violation both within and beyond the Standard Model (BSM). The interpretation of experimental EDM limits…
Wolumes is a fast and stand-alone computer program written in standard C that allows the measure of atom volumes in proteins. Its algorithm is a simple discretization of the space by means of a grid of points at 0.75 Angstroms from each…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Deep learning is an advanced technology that relies on large-scale data and complex models for feature extraction and pattern recognition. It has been widely applied across various fields, including computer vision, natural language…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
The convergent interests of different scientific disciplines, from biochemistry to electronics, toward the investigation of protein electrical properties, has promoted the development of a novel bailiwick, the so called proteotronics. The…
Quantum computing promises to speed up some of the most challenging problems in science and engineering. Quantum algorithms have been proposed showing theoretical advantages in applications ranging from chemistry to logistics optimization.…
Molecular science is governed by the dynamics of electrons, atomic nuclei, and their interaction with electromagnetic fields. A reliable physicochemical understanding of these processes is crucial for the design and synthesis of chemicals…
We initiate the systematic study of experimental quantum physics from the perspective of computational complexity. To this end, we define the framework of quantum algorithmic measurements (QUALMs), a hybrid of black box quantum algorithms…