Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Spontaneous transitions between non-equilibrium patterns are characterised by hydrodynamic calculations of ideal straight roll steady state heat convection. The calculations are tested quantitatively against existing experimental data. It…
Quantum systems driven by time-dependent Hamiltonians are considered here within the framework of steepest-entropy-ascent quantum thermodynamics (SEAQT) and used to study the thermodynamic characteristics of such systems. In doing so, a…
We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Efficient and accurate algorithm for partition function, free energy and thermal entropy calculations is of great significance in statistical physics and quantum many-body physics. Here we present an unbiased but low-technical-barrier…
The statistical mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each…
We describe the study of thermodynamics of materials using replica-exchange Wang-Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang-Landau Monte Carlo method. To evaluate the performance and…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
In this work, Landau's theory is revisited by renormalizing quadratic coefficients derived from nonlinear polynomial equations to account for system dimensionality. In this respect, the generated coefficients, which include an intrinsic…
We develop a theory for inferring equilibrium transition rates from trajectories driven by a time dependent force using results from stochastic thermodynamics. Applying the Kawasaki relation to approximate the nonequilibrium distribution…
The 2D toric code is a prototypical example that exhibits non-trivial topological properties and a ground state possessing a non-trivial topological order. Until now, all the cases studied in the literature have been in the stable…
This article focuses on a preaveraging description of polymer nonequilibrium stretching, where a single polymer undergoes a transient process from equilibrium to nonequilibrium steady state by pulling one chain end. The preaveraging method…
The density of states of continuous models is known to span many orders of magnitudes at different energies due to the small volume of phase space near the ground state. Consequently, the traditional Wang-Landau sampling which uses the same…
As far as we know, there is no flat-histogram algorithm to sample the stationary distribution of non-equilibrium stochastic processes. The present work addresses this gap by introducing a generalization of the Wang-Landau algorithm, applied…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
The problem of calculating the electron-positively charged particle correlation energy poses a challenge in the field of quantum chemistry beyond the adiabatic approximation. In this study, a toy model called Exotic Harmonium is developed…
In many statistical learning problems, the target functions to be optimized are highly non-convex in various model spaces and thus are difficult to analyze. In this paper, we compute \emph{Energy Landscape Maps} (ELMs) which characterize…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range…