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A phase transition indicates a sudden change in the properties of a large system. For temperature-driven phase transitions this is related to non-analytic behavior of the free energy density at the critical temperature: The knowledge of the…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
The Free-Energy Principle (FEP) [1-3] has been adopted in a variety of ambitious proposals that aim to characterize all adaptive, sentient, and cognitive systems within a unifying framework. Judging by the amount of attention it has…
Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…
Astrophysical observations of neutron stars probe the structure of dense nuclear matter and have the potential to reveal phase transitions at high densities. Most recent analyses are based on parametrized models of the equation of state…
We calculate analytically the probabilities for intuitive and counterintuitive transitions in a three-state system, in which two parallel energies are crossed by a third, tilted energy. The state with the tilted energy is coupled to the…
By using a previously established exact characterization of the ground state of random potential systems in the thermodynamic limit, we determine the ground and first excited energy levels of quantum random energy models, discrete and…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
A recent letter [Lin & Goldman, Phys. Rev. Lett. 106, 127003 (2011)] has presented experimental data in highly disordered thin films, which were interpreted as a quantum phase transition, an intriguing and surprising result for this system.…
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…
The sensitivity of polarization observables in the reaction $NN \to NN \phi$ slightly above the threshold is studied with respect to the details of the one-boson exchange model and a possible admixture of hidden strangeness in the nucleon.…
We introduce a novel characterization of phase transitions based on hypothesis testing. In our formulation, a phase transition is defined as the breakdown of statistical indistinguishability under vanishing parameter perturbations in the…
The dynamics of a system, consisting of a particle initially in a Gaussian state interacting with a field mode, under the action of repeated measurements performed on the particle, is examined. It is shown that regardless of its initial…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Phase transitions which occur at zero temperature when some non-thermal parameter like pressure, chemical composition or magnetic field is changed are called quantum phase transitions. They are caused by quantum fluctuations which are a…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
We study transition paths in energy landscapes over multi-categorical Potts configurations using the mean-field approach introduced by Mauri et al., {\em Phys Rev Lett 130, 158402 (2023)}. Paths interpolate between two fixed configurations…