Related papers: Enhanced Conformational Sampling using Replica Exc…
Inference-time control of diffusion models aims to steer model outputs to satisfy new constraints without retraining. Previous approaches have mostly relied on heuristic guidance or have been coupled with Sequential Monte Carlo (SMC) for…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models…
We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
The determination of efficient collective variables is crucial to the success of many enhanced sampling methods. As inspired by previous discrimination approaches, we first collect a set of data from the different metastable basins. The…
In recent years, pi-conjugated polymers are attracting considerable interest in view of their light-dependent torsional reorganization around the pi-conjugated backbone, which determines peculiar light-emitting properties. Motivated by the…
At fine lattice spacings, Markov chain Monte Carlo simulations of QCD and other gauge theories with or without fermions are plagued by slow modes that give rise to large autocorrelation times. This can lead to simulation runs that are…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
Atomistic simulations of thermodynamic properties of magnetic materials rely on an accurate modelling of magnetic interactions and an efficient sampling of the high-dimensional spin space. Recent years have seen significant progress with a…
When approaching the continuum limit in lattice QCD or other theories in a setup with topological sectors, conventional update algorithms experience a particularly severe form of critical slowing down that is caused by high action barriers…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what…
We extend replica exchange simulation in two ways, and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution -- i.e., between detailed and coarse-grained models.…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…