Related papers: Free energy reconstruction from steered dynamics w…
By the end of 2021, the renewable energy share of the global electricity capacity reached 38.3% and the new installations are dominated by wind and solar energy, showing global increases of 12.7% and 18.5%, respectively. However, both wind…
We introduce a method to obtain one-dimensional collective variables for studying rarely occurring transitions between two metastable states separated by a high free energy barrier. No previous information, not even approximated, on the…
Generative models and those with computationally intractable likelihoods are widely used to describe complex systems in the natural sciences, social sciences, and engineering. Fitting these models to data requires likelihood-free inference…
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
We propose a metadynamics-based (MetaD-based) approach for constructing the free energy surface (FES) of vacancy dynamics in crystals. In this approach, the vacancy FES can be constructed without explicitly defining a unique vacancy…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
In experiments and in simulations, the free energy of a state of a system can be determined from the probability that the state is occupied. However, it is often necessary to impose a biasing potential on the system so that high energy…
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this…
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely…
The Replica Exchange Wang-Landau Method is used to estimate the energy landscape of a polymer composed of a simple hydrophobic and polar sequence using the HP protein model. Calculations of state transitions between the energy levels of the…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
Thermodynamic properties can be in principle derived from the partition function, which, in many-atom systems, is hard to evaluate as it involves a sum on the accessible microscopic states. Recently, the partition function has been computed…
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with…
We propose a score-based generative algorithm for sampling from power-scaled priors and likelihoods within the Bayesian inference framework. Our algorithm enables flexible control over prior-likelihood influence without requiring retraining…
The role of the potential energy landscape in determining the relaxation dynamics of model clusters is studied using a master equation. Two types of energy landscape are examined: a single funnel, as exemplified by 13-atom Morse clusters,…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…