Related papers: Sampling Free Energy Surfaces as Slices by Combini…
Neural implicit representations have become a popular choice for modeling surfaces due to their adaptability in resolution and support for complex topology. While previous works have achieved impressive reconstruction quality by training on…
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecular behavior. These free energy surfaces are most commonly…
Metasurfaces are ultrathin, engineered materials composed of nanostructures that manipulate light in ways unattainable by natural materials. Recent advances have leveraged computational optimization, machine learning, and deep learning to…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
Multidimensional scaling (MDS) is a widely used approach to representing high-dimensional, dependent data. MDS works by assigning each observation a location on a low-dimensional geometric manifold, with distance on the manifold…
We propose an efficient and general strategy of metadynamics (MetaD) for investigating interstitial diffusion in a crystal by exploiting crystallographic symmetry. Assuming complete ignorance of the diffusion phenomenon of interest, the…
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…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
We explore a versatile technique for inverse designing 2D photonic crystal metasurfaces. These surfaces, known for their ability to manipulate light-matter interactions, can be precisely controlled to achieve specific functionalities. The…
The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
Understanding the impact of extractant functionalization in solvent extraction is essential to guide the development of better separations processes. Traditionally, computational extractant design uses electronic structure calculations to…
Dataset distillation compresses large training sets into compact synthetic datasets while preserving downstream performance. As modern systems increasingly operate on paired vision-language inputs, multimodal distillation must preserve…
Multispectral transmission imaging provides strong benefits for early breast cancer screening. The frame accumulation method addresses the challenge of low grayscale and signal-to-noise ratio resulting from the strong absorption and…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Free surface flow problems including mixing processes in dam break flows and wave breaking phenomena are characterized by large deformation of the free surface. As such, they cannot be easily investigated by analytical and numerical mesh…
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a…
Temperature-accelerated sliced sampling (TASS) is a well-established enhanced sampling method that facilitates exhaustive exploration of high-dimensional collective variable (CV) space through directed sampling employing a combination of…