Related papers: Reweighted ensemble dynamics simulations: theory, …
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…
A novel method combining maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here we focus on the Karplus parameters for RNA systems, which relate the…
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
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…
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium processes can be described by suitable subsets of the equilibrium…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
Weighted ensemble (WE) is an enhanced path-sampling method that is conceptually simple, widely applicable, and statistically exact. In a WE simulation, an ensemble of trajectories is periodically pruned or replicated to enhance sampling of…
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist to obtain the thermodynamic functions for such systems. But…
Predictive simulations of complex systems are essential for applications ranging from weather forecasting to drug design. The veracity of these predictions hinges on their capacity to capture the effective system dynamics. Massively…
There is a great need for improved statistical sampling in a range of physical, chemical and biological systems. Even simulations based on correct algorithms suffer from statistical error, which can be substantial or even dominant when slow…
The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules.We present a method to obtain path ensemble averages of a perturbed…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…