Related papers: Weighted Ensemble Path Sampling for Multiple React…

With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…

The imbalanced data classification remains a vital problem. The key is to find such methods that classify both the minority and majority class correctly. The paper presents the classifier ensemble for classifying binary, non-stationary and…

Atomic nuclei are composite systems, and they may be dynamically excited during nuclear reactions. Such excitations are not only relevant to inelastic scattering but they also affect other reaction processes such as elastic scattering and…

Ensembling has proven to be a powerful technique for boosting model performance, uncertainty estimation, and robustness in supervised learning. Advances in self-supervised learning (SSL) enable leveraging large unlabeled corpora for…

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…

We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely…

Merging various task-specific Transformer-based models trained on different tasks into a single unified model can execute all the tasks concurrently. Previous methods, exemplified by task arithmetic, have been proven to be both effective…

For Paley-Wiener functions on weighted combinatorial finite or infinite graphs we develop a weighted sampling theory in which samples are defined as inner products with weight functions (measuring devices). Three reconstruction methods are…

We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…

We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…

The adaptive multi-channel method is applied to derive probability distributions from data samples. Moreover, an explicit algorithm is introduced, for which both the channel weights and the channels themselves are adaptive, and which can be…

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a…

The study of the rare transitions that take place between long lived metastable states is a major challenge in molecular dynamics simulations. Many of the methods suggested to address this problem rely on the identification of the slow…

The most efficient MC weights for the calculation of physical, canonical expectation values are not necessarily those of the canonical ensemble. The use of suitably generalized ensembles can lead to a much faster convergence of the…

Joining records with all other records that meet a linkage condition can result in an astronomically large number of combinations due to many-to-many relationships. For such challenging (acyclic) joins, a random sample over the join result…

We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…

The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…