Related papers: Guidelines for the Calculation of Bound Molecular …
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the…
Monitoring the dynamics processes in combustors is crucial for safe and efficient operations. However, in practice, only limited data can be obtained due to limitations in the measurable quantities, visualization window, and temporal…
In statistics, it is important to have realistic data sets available for a particular context to allow an appropriate and objective method comparison. For many use cases, benchmark data sets for method comparison are already available…
Dielectric spectra are typically obtained in molecular dynamics (MD) simulations by analyzing the fluctuations, in the absence of an applied electric field, of the total dipole moment of the simulation box. We compare this standard method…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Interpretation of…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
Illuminant estimation aims to infer scene illumination from image measurements despite intrinsic ambiguities between surface reflectance and lighting. Most existing methods operate on trichromatic RGB images and are therefore fundamentally…
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. Such practice is needed in atomistic simulations of complex…
The ideal spectral averaging method depends on one's science goals and the available information about one's data. Including low-quality data in the average can decrease the signal-to-noise ratio (SNR), which may necessitate an optimization…
In the context of computer models, calibration is the process of estimating unknown simulator parameters from observational data. Calibration is variously referred to as model fitting, parameter estimation/inference, an inverse problem, and…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
Accurate simulations of molecules require high-level electronic-structure theory in combination with rigorous methods for approximating the quantum dynamics. Machine-learning approaches can significantly reduce the computational expense of…
Lattice-Boltzmann (LB) simulations are a common tool to numerically estimate the permeability of porous media. For valuable results, the porous structure has to be well resolved resulting in a large computational effort as well as high…
Particle suspensions are ubiquitous in our daily life, but are not well understood due to their complexity. During the last twenty years, various simulation methods have been developed in order to model these systems. Due to varying…