Related papers: Automated and optimally FRET-assisted structural m…
An experimental strategy has been developed specifically for the study of composition-dependent phase behavior in multi-component artificial membranes. The strategy is based on steady-state measurements of fluorescence resonance energy…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…
This paper proposes an adaptive random experiment design (ARED) algorithm that can be applied to optimize the multiple factors and levels experiments. The algorithm takes real-time model error as the adaptive condition, and outputs a model…
Real-time simulation enables the understanding of system operating conditions by evaluating simulation models of physical components running synchronized at the real-time wall clock. Leveraging the real-time measurements of comprehensive…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…
Cryo-electron microscopy can now routinely deliver atomic resolution structures for a variety of biological systems. The relevance and value of these structures is directly related to their ability to help rationalize experimental…
Computer simulations are becoming an essential tool in many scientific fields from molecular dynamics to aeronautics. In glaciology, future predictions of sea level change require input from ice sheet models. Due to uncertainties in the…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
A meta-model of the input-output data of a computationally expensive simulation is often employed for prediction, optimization, or sensitivity analysis purposes. Fitting is enabled by a designed experiment, and for computationally expensive…
A computer model can be used for predicting an output only after specifying the values of some unknown physical constants known as calibration parameters. The unknown calibration parameters can be estimated from real data by conducting…
The structural design process for buildings is time-consuming and laborious. To automate this process, structural engineers combine optimization methods with simulation tools to find an optimal design with minimal building mass subject to…
Increasing complexity in the power system and the transformation towards a smart grid lead to the necessity of new tools and methods for the development and testing of new technologies. One testing method is co-simulation, which allows…
Computational models are powerful tools for understanding human cognition and behavior. They let us express our theories clearly and precisely, and offer predictions that can be subtle and often counter-intuitive. However, this same…
It is important to accurately model materials' properties at lower length scales (micro-level) while translating the effects to the components and/or system level (macro-level) can significantly reduce the amount of experimentation required…
Single-molecule F\"{o}rster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated…
Response surface designs are usually described as being run under complete randomization of the treatment combinations to the experimental units. In practice, however, it is often necessary or beneficial to run them under some kind of…
The design space for inertial confinement fusion (ICF) experiments is vast and experiments are extremely expensive. Researchers rely heavily on computer simulations to explore the design space in search of high-performing implosions.…
Fluorescence spectroscopy and modeling provide powerful means to characterize biomacromolecular structures, dynamics, and interactions. F\"orster resonance energy transfer serves as a key technique for this due to its nanometer-scale…