Related papers: Quantum conformational transition in biological ma…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We consider the quantum dynamics of a test particle in noncommutative space under the influence of linearized gravitational waves in the long wave-length and low-velocity limit. A prescription for quantizing the classical Hamiltonian for…
Non-Hermitian Hamiltonians are relevant to describe the features of a broad class of physical phenomena, ranging from photonics and atomic and molecular systems to nuclear physics and mesoscopic electronic systems. An important question…
A procedure for calculation of rotation-vibration states of medium sized molecules is presented. It combines the advantages of variational calculations and perturbation theory. The vibrational problem is solved by diagonalizing a…
Conformational transitions in macromolecular complexes often involve the reorientation of lever-like structures. Using a simple theoretical model, we show that the rate of such transitions is drastically enhanced if the lever is bendable,…
Can the properties of the thermodynamic limit of a many-body quantum system be extrapolated by analysing a sequence of finite-size cases? We present a model for which such an approach gives completely misleading results: a translationally…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
A dynamical quantum phase transition can occur during time evolution of sudden quenched quantum systems across a phase transition. It corresponds to the nonanalytic behavior at a critical time of the rate function of the quantum state…
We develop a general approach for monitoring and controlling evolution of open quantum systems. In contrast to the master equations describing time evolution of density operators, here, we formulate a dynamical equation for the evolution of…
The stability of quantum systems to perturbations of the Hamiltonian is studied. This stability is quantified by the fidelity. Dependence of fidelity on the initial state as well as on the dynamical properties of the system is considered.…
Suppose a quantum system starts to evolve under a Hamiltonian from some initial state. When for the first time, will an observable attain a preassigned value? To answer this question, one method often adopted is to make instantaneous…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We introduce a type of quantum dissipation -- local quantum friction -- by adding to the Hamiltonian a local potential that breaks time-reversal invariance so as to cool the system. Unlike the Kossakowski-Lindblad master equation, local…
This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is…
At low temperature a thermodynamic system undergoes a phase transition when a physical parameter passes through a singularity point of the free energy, corresponding to formation of a new order. At high temperature the thermal fluctuations…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
We develop a computational method to learn a molecular Hamiltonian matrix from matrix-valued time series of the electron density. As we demonstrate for three small molecules, the resulting Hamiltonians can be used for electron density…
The decay rate for a particle in a metastable cubic potential is investigated in the quantum regime by the Euclidean path integral method in semiclassical approximation. The imaginary time formalism allows one to monitor the system as a…