Related papers: Quantum conformational transition in biological ma…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…
The vibrational dynamics of protein folding is analyzed in the framework of Tsallis thermostatistics. The generalized partition functions, internal energies, free energies and temperature factor (or Debye-Waller factor) are calculated. It…
In optimal quantum-mechanical evolutions, motion can take place along paths of minimal length within an optimal time frame. Alternatively, optimal evolutions may occur along established paths without any waste of energy resources and…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
We propose a relationship between thermodynamic phase transitions and ground-state quantum phase transitions in systems with variable Hamiltonian parameters. It is based on a link between zeros of the canonical partition function at complex…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Transition metal complexes for photochemical applications often feature a high density of electron-vibrational states characterized by nonadiabatic and spin-orbit couplings. Overall, the dynamics after photoexcitation is shaped by rapid…
We characterize excited state quantum phase transitions in the two dimensional limit of the vibron model with the quantum fidelity susceptibility, comparing the obtained results with the information provided by the participation ratio. As…
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…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
Understanding molecular state evolution is central to many disciplines, including molecular dynamics, precision measurement, and molecule-based quantum technology. Details of the evolution are obscured when observing a statistical ensemble…
Adaptive perturbation is a new method for perturbatively computing the eigenvalues and eigenstates of quantum mechanical Hamiltonians that heretofore were not believed to be obtainable by such methods. The novel feature of adaptive…
Protein folding is a central challenge in computational biology, with important applications in molecular biology, drug discovery and catalyst design. As a hard combinatorial optimisation problem, it has been studied as a potential target…