Related papers: Analysis of Two-State Folding Using Parabolic Appr…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
Nuclear binding energies and two-neutron separation energies are analyzed starting from the liquid-drop model and the nuclear shell model in order to describe the global trends of the above observables. We subsequently concentrate on the…
Protein denaturing induced by supercooling is interpreted as a process where some or all internal symmetries of the native protein are spontaneously broken. Hence, the free-energy potential corresponding to a folding-funnel landscape…
Motivated by questions of present interest in nuclear and condensed matter physics we consider the superposition of a diagonal matrix with independent random entries and a GUE. The relative strength of the two contributions is determined by…
We consider the Solid-On-Solid model interacting with a wall, which is the statistical mechanics model associated with the integer-valued field $(\phi(x))_{x\in \mathbb Z^2}$, and the energy functional $$V(\phi)=\beta \sum_{x\sim…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
A nonperturbative electron transfer rate theory is developed based on the reduced density matrix dynamics, which can be evaluated readily for the Debye solvent model without further approximation. Not only does it recover for reaction rates…
We study the evolution of a classical harmonic chain with nearest-neighbor interactions starting from domain wall initial conditions. The initial state is taken to be either a product of two Gibbs Ensembles (GEs) with unequal temperatures…
The entanglement of general pure Gaussian two-mode states is examined in terms of the coefficients of the quadrature components of the wavefunction. The entanglement criterion and the entanglement of formation are directly evaluated as a…
We study the dynamics of a two-level crossing model with a parabolic separation of the diabatic energies. The solutions are expressed in terms of the tri-confluent Heun equations --- the generalization of the confluent hypergeometric…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
We develop a general perturbative theory of finite-coupling quantum thermometry up to second order in probe-sample interaction. By assumption, the probe and sample are in thermal equilibrium, so the probe is described by the mean-force…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
We study the equivalence of ensembles for stationary measures of interacting particle systems with two conserved quantities and unbounded local state space. The main motivation is a condensation transition in the zero-range process which…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
The off-diagonal disorder caused by random spin orientations in the paramagnetic (PM) state of the double exchange (DE) model is described by using the coherent-potential-approximation (CPA), which is combined with the variational…
We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…