Related papers: Quantum conformational transition in biological ma…
The coupling of electronic and vibrational motion is studied by two canonical transformations namely normal coordinate transformation and momentum transformation on molecular Hamiltonian. It is shown that by these transformations we can…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
A quantum phase transition is usually achieved by tuning physical parameters in a Hamiltonian at zero temperature. Here, we demonstrate that the ground state of a topological phase itself encodes critical properties of its transition to a…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
We consider the possibility of topological quantum phase transitions of ultracold fermions in optical lattices, which can be studied as a function of interaction strength or atomic filling factor (density). The phase transitions are…
The combined quantum electron-nuclear dynamics is often associated with the Born-Huang expansion of the molecular wave function and the appearance of nonadiabatic effects as a perturbation. On the other hand, native multicomponent…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
We consider the problem of finding the energy minimum of a complex quantum Hamiltonian by employing a non-Markovian bath prepared in a low energy state. The energy minimization problem is thus turned into a thermodynamic cooling protocol in…
Nonrelativistically forbidden, single-photon transition rates between low lying states of the helium atom are rigorously derived within quantum electrodynamics theory. Equivalence of velocity and length gauges, including relativistic…
Phase transitions are fundamental in nature. A small parameter change near a critical point leads to a qualitative change in system properties. Across a regular phase transition, the system remains in thermal equilibrium and, therefore,…
We characterize the high-temperature thermodynamics of rotating bosons and fermions in two- (2D) and three-dimensional (3D) isotropic harmonic trapping potentials. We begin by calculating analytically the conventional virial coefficients…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Quantum computation of vibrational properties of molecules is a promising platform to obtain computational advantages for computational chemistry. However, fault-tolerant quantum computations of vibrational properties remain a relatively…
At room temperature, low frequency vibrations at far-infrared frequencies are thermally excited ($k_B T > h \nu$) and not restricted to harmonic fluctuations around a single potential energy minimum. For folded proteins, these intrinsically…