Related papers: Selection originating from protein foldability: I.…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Boltzmann generators approach the sampling problem in many-body physics by combining a normalizing flow and a statistical reweighting method to generate samples of a physical system's equilibrium density. The equilibrium distribution is…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We use computer simulations to study the thermodynamic properties of a glass former in which a fraction $c$ of the particles has been permanently frozen. By thermodynamic integration, we determine the Kauzmann, or ideal glass transition,…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
The Z method is a popular atomistic simulation method for determining the melting temperature where a sequence of molecular dynamics runs are carried out to target the lowest system energy where the solid always melts. Homogeneous melting…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
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…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Randomness is ubiquitous in many applications across data science and machine learning. Remarkably, systems composed of random components often display emergent global behaviors that appear deterministic, manifesting a transition from…
We prove that an effective temperature naturally emerges from the algorithmic structure of a regular universal Turing machine (UTM), without introducing any external physical parameter. In particular, the redundancy growth of the machine's…
Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…
A theory for the nonlinear energy response of a system subjected to a heat bath is developed when the temperature of the heat bath is modulated sinusoidally. The theory is applied to a model glass forming system, where the landscape is…
Accurate prediction of electron temperature ($T_{\rm e}$) in non-equilibrium {plasma} flows is critical, yet hampered by inadequate models for electron heating from vibrationally excited states. Prior models often relied on ad-hoc scaling…