Related papers: Protein Folding as a Quantum Transition Between Co…

A quantum system can undergo a continuous phase transition at the absolute zero of temperature as some parameter entering its Hamiltonian is varied. These transitions are particularly interesting for, in contrast to their classical finite…

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…

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…

The nuclear wobbling motion is studied from a microscopic viewpoint. It is shown that the expressions not only of the excitation energy but also of the electromagnetic transition rate in the microscopic RPA framework can be cast into the…

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

An approach to the simulation of locally interacting systems is demonstrated and assayed. The proposal is built upon the concept of folding of bosonic modes previously introduced in the context of linear dynamics and can be seen as an…

The quantum phase transitions in the one-dimensional asymmetric Hubbard model are investigated with the bosonization approach. The conditions for the phase transition from density wave to phase separation, the correlation functions and…

Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…

Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…

Stochastic systems feature, in general, both coherent dynamics and incoherent transitions between different states. We propose a method to identify the coherent part in the full counting statistics for the transitions. The proposal is…

This article covers few selected aspects of quantum theory of molecular rotations and vibrations. Triatomic molecules are the simplest systems, which show qualitative characteristics of larger polyatomic molecules. On the minimal example of…

A time-dependent approach is used to explore inelastic effects during electron transport through few-level systems. We study a tight-binding chain with one and two sites connected to vibrations. This simple but transparent model gives…

We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In…

Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…

Quantum phase transitions occur at zero temperature, when the ground state of a Hamiltonian undergoes a qualitative change as a function of a control parameter. We consider a particularly interesting system with competing one-, two- and…

The possibility of an atomic detection of gravitational waves on earth is considered. The combination of extremely high lifetimes and resulting small radiative transition probabilities with rapidly growing interaction strength for Rydberg…

We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals and hot solids. Promising results from this method were recently…

The accuracy of the noninteracting electron approximation is examined for a model of vibrationally coupled electron transport in single molecule junction. In the absence of electronic-vibrational coupling, steady state transport in this…