Related papers: Multidimensional Replica Exchange simulations for …
This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for efficient simulation of moderately stiff reactive problems. This framework features an elaborate subcycling-in-time algorithm along with a specialized…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
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…
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…
Simulations have played a critical role in the advancement of our knowledge of magnetic reconnection. However, due to the inherently multiscale nature of reconnection, it is impossible to simulate all physics at all scales. For this reason,…
We present a new three-dimensional radiative transfer (RT) code, RADAMESH, based on a ray-tracing, photon-conserving and adaptive (in space and time) scheme. RADAMESH uses a novel Monte Carlo approach to sample the radiation field within…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown…
Molecular dynamics (MD) simulations involving reactive potentials can be used to model material failure. The empirical potentials which are used in such simulations are able to adapt to the atomic environment, at the expense of a…
We present an adaptive multi-GPU Exchange Monte Carlo method designed for the simulation of the 3D Random Field Model. The algorithm design is based on a two-level parallelization scheme that allows the method to scale its performance in…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
Advection-Diffusion-Reaction (ADR) Partial Differential Equations (PDEs) appear in a wide spectrum of applications such as chemical reactors, concentration flows, and biological systems. A large number of these applications require the…
We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of…
Meshless methods approximate operators in a specific node as a weighted sum of values in its neighbours. Higher order approximations of derivatives provide more accurate solutions with better convergence characteristics, but they come at…
Hydrogen is vital for sectors like chemicals and others, driven by the need to reduce carbon emissions. Proton Electrolyte Membrane Water Electrolysis (PEMWE) is a key technology for the production of green hydrogen under fluctuating…
Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems.…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
In the study of non-adiabatic chemical processes such as photocatalysis and photosynthesis, non-adiabatic molecular dynamics (NAMD) is an indispensable theoretical tool, which requires precise potential energy surfaces (PESs) of ground and…