Related papers: Conformational Entropy as Collective Variable for …
We present and test a general-purpose code, called PPASPH, for evolving self-gravitating fluids in astrophysics, both with and without a collisionless component. In PPASPH, hydrodynamical properties are computed by using the SPH (Smoothed…
Smoothed particle hydrodynamics (SPH) is typically used for barotropic fluids, where the pressure depends only on the local mass density. Here, we show how to incorporate the entropy into the SPH, so that the pressure can also depend on the…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…
We consider a three dimensional, generalized version of the original SPP model for collective motion. By extending the factors influencing the ordering, we investigate the case when the movement of the self-propelled particles (SPP-s)…
Generating a data set that is representative of the accessible configuration space of a molecular system is crucial for the robustness of machine learned interatomic potentials (MLIP). However, the complexity of molecular systems,…
The asymptotic behaviour near phase transitions can be suitably characterized by the scaling of $\Delta s/Q^2$ with $\epsilon=1-T/T_c$, where $\Delta s$ is the excess entropy and $Q$ is the order parameter. As $\Delta s$ is obtained by…
While many Particle Swarm Optimization (PSO) algorithms only use fitness to assess the performance of particles, in this work, we adopt Surprisingly Popular Algorithm (SPA) as a complementary metric in addition to fitness. Consequently,…
The description of chemical processes at the molecular level is often facilitated by use of reaction coordinates, or collective variables (CVs). The CV measures the progress of the reaction and allows the construction of profiles that track…
The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradigm of mapping one…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
The laws of thermodynamics apply to biophysical systems on the nanoscale as described by the framework of stochastic thermodynamics. This theory provides universal, exact relations for quantities like work, which have been verified in…
Current state-of-the-art generative models map noise to data distributions by matching flows or scores. A key limitation of these models is their inability to readily integrate available partial observations and additional priors. In…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Atmospheric systems incorporating thermal dynamics must be stable with respect to both energy and entropy. While energy conservation can be enforced via the preservation of the skew-symmetric structure of the Hamiltonian form of the…
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…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collective variables and is gradually modified according to the…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…