Related papers: Adaptive ensemble simulations of biomolecules
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Numerical optimization of complex systems benefits from the technological development of computing platforms in the last twenty years. Unfortunately, this is still not enough, and a large computational time is still necessary when…
With the increase of research in self-adaptive systems, there is a need to better understand the way research contributions are evaluated. Such insights will support researchers to better compare new findings when developing new knowledge…
Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Ensemble calculations are essential for systems with uncertain data but require substantial increase in computational resources. This increase severely limits ensemble size. To reach beyond current limits, we present a first-order…
Adaptive optics systems are essential on all large telescopes where image quality is important. These are complex systems with many design parameters requiring optimisation before good performance can be achieved. The simulation of adaptive…
Model selection is a strategy aimed at creating accurate and robust models. A key challenge in designing these algorithms is identifying the optimal model for classifying any particular input sample. This paper addresses this challenge and…
An empirical study was carried out to compare different implementations of ensemble models aimed at improving prediction in spectroscopic data. A wide range of candidate models were fitted to benchmark datasets from regression and…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
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…
Ongoing investigations to introduce software techniques suitable to support new experimental requirements for multi-scale simulation are discussed.
Background: Advanced adaptive randomised clinical trials are increasingly used. Compared to their conventional counterparts, their flexibility may make them more efficient, increase the probability of obtaining conclusive results without…
This paper develops an adaptive generic proximal bundle method, shows its complexity, and presents numerical experiments comparing this method with two bundle methods on a set of optimization problems.
Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…
In this article, a new generic higher-order finite-element framework for massively parallel simulations is presented. The modular software architecture is carefully designed to exploit the resources of modern and future supercomputers.…
One of the difficulties in developing collective adaptive systems is the challenge of simultaneously engineering both the desired resilient behaviour of the collective and the details of its implementation on individual devices. Aggregate…
Like with most large-scale systems, the evaluation of quantitative properties of collective adaptive systems is an important issue that crosscuts all its development stages, from design (in the case of engineered systems) to runtime…
Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…