Related papers: MADNESS: A Multiresolution, Adaptive Numerical Env…
We describe the adaptive resolution multiscale method AdResS. The conceptual evolution as well as the improvements of its technical efficiency are described step by step, with an explicit reference to current limitations and open problems.
The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea…
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
Multidimensional scaling (MDS) is a dimensionality reduction tool used for information analysis, data visualization and manifold learning. Most MDS procedures embed data points in low-dimensional Euclidean (flat) domains, such that…
Due to the unprecedented depth of the upcoming ground-based Legacy Survey of Space and Time (LSST) at the Vera C. Rubin Observatory, approximately two-thirds of the galaxies are likely to be affected by blending - the overlap of physically…
Multidimensional scaling (MDS) is a popular dimensionality reduction techniques that has been widely used for network visualization and cooperative localization. However, the traditional stress minimization formulation of MDS necessitates…
Computational materials science produces large quantities of data, both in terms of high-throughput calculations and individual studies. Extracting knowledge from this large and heterogeneous pool of data is challenging due to the wide…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Key questions that scientists and engineers typically want to address can be formulated in terms of predictive science. Questions such as: "How well does my computational model represent reality?", "What are the most important parameters in…
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to…
The proliferation of pre-trained models has given rise to a wide array of specialised, fine-tuned models. Model merging aims to merge the distinct capabilities of these specialised models into a unified model, requiring minimal or even no…
We present MADLens a python package for producing non-Gaussian lensing convergence maps at arbitrary source redshifts with unprecedented precision. MADLens is designed to achieve high accuracy while keeping computational costs as low as…
Multidimensional scaling (MDS) is a family of methods that embed a given set of points into a simple, usually flat, domain. The points are assumed to be sampled from some metric space, and the mapping attempts to preserve the distances…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
The explosive demand for artificial intelligence (AI) workloads has led to a significant increase in silicon area dedicated to lower-precision computations on recent high-performance computing hardware designs. However, mixed-precision…
Multidimensional Scaling (MDS) is a classic technique that seeks vectorial representations for data points, given the pairwise distances between them. However, in recent years, data are usually collected from diverse sources or have…