Related papers: Adaptive resolution molecular dynamics simulation …
A four dimensional systematic mathematical approach for investigating propagation and coupling of wave modes in a slowly varying (in all space directions and time) anisotropic, absorbing plasma is represented. The formalism is especially…
We use molecular dynamics simulations to probe the rotational dynamics of the SPC/E model of water for a range of temperatures down to 200 K, 13 K above to the mode coupling temperature. We find that rotational dynamics is spatially…
Sufficient dimension reduction [J. Amer. Statist. Assoc. 86 (1991) 316-342] has long been a prominent issue in multivariate nonparametric regression analysis. To uncover the central dimension reduction space, we propose in this paper an…
We report the optical imaging of a single atom with nanometer resolution using an adaptive optical alignment technique that is applicable to general optical microscopy. By decomposing the image of a single laser-cooled atom, we identify and…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Domain adaptation and generative modelling have collectively mitigated the expensive nature of data collection and labelling by leveraging the rich abundance of accurate, labelled data in simulation environments. In this work, we study the…
We propose a new randomized optimization method for high-dimensional problems which can be seen as a generalization of coordinate descent to random subspaces. We show that an adaptive sampling strategy for the random subspace significantly…
We propose an adaptive scheme of broadening the discrete spectral data from numerical renormalization group (NRG) calculations to improve the resolution of dynamical properties at finite energies. While the conventional scheme overbroadens…
This work presents a camera model for refractive media such as water and its application in underwater visual-inertial odometry. The model is self-calibrating in real-time and is free of known correspondences or calibration targets. It is…
We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple…
Previous studies have used numerical methods to optimize the hyperpolarizability of a one-dimensional quantum system. These studies were used to suggest properties of one-dimensional organic molecules, such as the degree of modulation of…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
In this paper we investigate the possibility to detect the hypothesized liquid-liquid critical point of water in supercooled aqueous solutions of salts. Molecular dynamics computer simulations are conducted on bulk TIP4P water and on an…
An adaptive algorithm for computing eigenmodes and propagation constants of optical fibers is proposed. The algorithm is built using a dual-weighted residual error estimator. The residuals are based on the eigensystem for leaky hybrid modes…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Atomistic simulations with methods such as molecular dynamics are extremely powerful tools to understand nanoscale dynamical behavior. The resulting trajectories, by the virtue of being embedded in a high-dimensional configuration space,…
Molecular dynamics simulations are used to study fluidization of a vertically vibrated, three-dimensional shallow granular layer. As the container acceleration is increased above g, the granular temperature and root mean square particle…