Related papers: Looking into DNA breathing dynamics via quantum ph…
We develop a rigorous treatment of discontinuous stochastic unitary evolution for a system of quantum particles that interacts singularly with quantum "bubbles" at random instants of time. This model of a "cloud chamber" allows to watch and…
We simulate the dynamics of a quantum dot coupled to the single resonating mode of a metal nano-particle. Systems like this are known as metamolecules. In this study, we consider a time-dependent driving field acting onto the metamolecule.…
Convergence conditions for quantum annealing are derived for optimization problems represented by the Ising model of a general form. Quantum fluctuations are introduced as a transverse field and/or transverse ferromagnetic interactions, and…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
We study the Wheeler-DeWitt quantization of a spatially flat Friedmann-Lema\^itre-Robertson-Walker (FLRW) universe with pressureless dust (modeled via the Brown-Kucha\v{r} formalism) and a dynamical cosmological constant $\Lambda$ treated…
The phase space dynamics of dissipative quantum systems in strongly condensed phase is considered. Based on the exact path integral approach it is shown that the Wigner transform of the reduced density matrix obeys a time evolution equation…
The behavior of a heavy tagged intruder immersed in a bath of particles evolving under ballistic annihilation dynamics is investigated. The Fokker-Planck equation for this system is derived and the peculiarities of the corresponding…
We develop a trajectory-based approach for excited-state molecular dynamics simulations of systems subject to an external periodic drive. We combine the exact-factorization formalism, allowing to treat electron-nuclear systems in…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
In this work we investigate the ground state and the dissipative quantum dynamics of interacting charged particles in an external potential at finite temperature. The recently devised time-dependent quantum Monte Carlo (TDQMC) method allows…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
We show how the quantum analog of the Fokker-Planck equation for describing Brownian motion can be obtained as the diffusive limit of the quantum linear Boltzmann equation. The latter describes the quantum dynamics of a tracer particle in a…
A general quantum adiabatic theorem with and without the time-dependent orthogonalization is proven, which can be applied to understand the origin of activation energies in chemical reactions. Further proofs are also developed for the…
The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally…
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic…
We study the real time dynamics of a quantum system with potential barrier coupled to a heat-bath environment. Employing the path integral approach an evolution equation for the time dependent density matrix is derived. The time evolution…
The Fokker_Planck equation can be derived in a consistent manner through a microscopic approach based on a unified scheme of classical and quantum mechanics. Here we shall derive it through a purely quantum mechanical approach based on the…
A structure of generator of a quantum dynamical semigroup for the dynamics of a test particle interacting through collisions with the environment is considered, which has been obtained from a microphysical model. The related master-equation…