Related papers: Toward end-to-end quantum simulation for protein d…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
We present a comprehensive end-to-end framework for simulating the real-time dynamics of chemical systems on a fault-tolerant quantum computer, incorporating both electronic and nuclear quantum degrees of freedom. An all-particle simulation…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
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…
Quantum algorithms for simulating electronic ground states are slower than popular classical mean-field algorithms such as Hartree-Fock and density functional theory, but offer higher accuracy. Accordingly, quantum computers have been…
We present an end-to-end quantum algorithm for simulating nonlinear dynamics described by a system of stochastic dissipative differential equations with a quadratic nonlinearity. The stochastic part of the system is modeled by a Gaussian…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Quantum simulation is a potentially powerful application of quantum computing, holding the promise to be able to emulate interesting quantum systems beyond the reach of classical computing methods. Despite such promising applications, and…
We propose and analyze a sample-efficient protocol to estimate the fidelity between an experimentally prepared state and an ideal target state, applicable to a wide class of analog quantum simulators without advanced sophisticated…
Due to complexity of the systems and processes it addresses, the development of computational quantum physics is influenced by the progress in computing technology. Here we overview the evolution, from the late 1980s to the current year…
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…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
The theoretical investigation of non-adiabatic processes is hampered by the complexity of the coupled electron-nuclear dynamics beyond the Born-Oppenheimer approximation. Classically, the simulation of such reactions is limited by the…
Background: Understanding electronic interactions in protein active sites is fundamental to drug discovery and enzyme engineering, but remains computationally challenging due to exponential scaling of quantum mechanical calculations.…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We explore how the fundamental problems in quantum molecular dynamics can be modelled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes…
Simulating the dynamics of non-equilibrium matter under extreme conditions lies beyond the capabilities of classical computation alone. Remarkable advances in quantum information science and technology are profoundly changing how we…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Quantum computing has the potential to revolutionize multiple fields by solving complex problems that can not be solved in reasonable time with current classical computers. Nevertheless, the development of quantum computers is still in its…
We show that optimal control of the electron dynamics is able to prepare molecular ground states, within chemical accuracy, with evolution times approaching the bounds imposed by quantum mechanics. We propose a specific parameterization of…