Related papers: Quantum conformational transition in biological ma…
The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…
Quantum thermodynamics has emerged as a central field for understanding how energy conversion processes occur in microscopic systems. In these systems, effects such as coherence, entanglement, and non-Markovianity play key roles. In this…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
Quantum phase transitions between competing ground-state shapes of atomic nuclei with an odd number of protons or neutrons are investigated in a microscopic framework based on nuclear energy density functional theory and the…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
The perturbative approach was adopted to develop a temperature-dependent version of non-relativistic quantum mechanics in the limit of low-enough temperatures. A generalized, self-consistent Hamiltonian was therefore constructed for an…
Efficient sampling from ensembles of Hamiltonian cycles is critical for predicting the thermodynamic properties of compact polymers, with applications including modeling protein and RNA folding and designing soft materials. Although…
We consider measurement-based quantum computation using the state of a spin-lattice system in equilibrium with a thermal bath and free to evolve under its own Hamiltonian. Any single qubit measurements disturb the system from equilibrium…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We derive quantum kinetic equations for fermions in a homogeneous time-dependent background in presence of decohering collisions, by use of the Schwinger-Keldysh CTP-formalism. The quantum coherence (between particles and antiparticles) is…
Quantum shape-phase transitions in finite nuclei are considered in the framework of the interacting boson model. Critical-point Hamiltonians for first- and second-order transitions are identified by resolving them into intrinsic and…
We derive an electron-vibration model Hamiltonian in a quantum chemical framework, and explore the extent to which such a Hamiltonian can capture key effects of nonadiabatic dynamics. The model Hamiltonian is a simple two-body operator, and…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
We develop a perturbation theory of quantum (and classical) master equations with slowly varying parameters, applicable to systems which are externally controlled on a time scale much longer than their characteristic relaxation time. We…
We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that…
We develop a classical mapping approach suitable to describe vibrationally coupled charge transport in molecular junctions based on the Cartesian mapping for many-electron systems [J. Chem. Phys. 137, 154107 (2012)]. To properly describe…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
An effective Hamiltonian describing interaction between generic "fast" and a "slow" systems is obtained in the strong interaction limit. The result is applied for studying the effect of quantum phase transition as a bifurcation of the…