Related papers: Resolution exchange simulation
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
In engineering, it is a common desire to couple existing simulation tools together into one big system by passing information from subsystems as parameters into the subsystems under influence. As executed at fixed time points, this data…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
Emulation has been successfully applied across a wide variety of scientific disciplines for efficiently analysing computationally intensive models. We develop known boundary emulation strategies which utilise the fact that, for many…
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…
In this article we present an algorithm to efficiently evaluate the exchange matrix in periodic systems when Gaussian basis set with pseudopotentials are used. The usual algorithm for evaluating exchange matrix scales cubically with the…
Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
Computational models are quantitative representations of systems. By analyzing and comparing the outputs of such models, it is possible to gain a better understanding of the system itself. Though as the complexity of model outputs…
Reciprocal transformations mix the role of the dependent and independent variables to achieve simpler versions or even linearized versions of nonlinear PDEs. These transformations help in the identification of a plethora of PDEs available…