Related papers: MDRefine: a Python package for refining Molecular …
Model-free data-driven computational mechanics (DDCM) is a new paradigm for simulations in solid mechanics. The modeling step associated to the definition of a material constitutive law is circumvented through the introduction of an…
This paper introduces PatchRefiner, an advanced framework for metric single image depth estimation aimed at high-resolution real-domain inputs. While depth estimation is crucial for applications such as autonomous driving, 3D generative…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be…
Neural Posterior Estimation (NPE) enables rapid parameter inference for complex simulators with intractable likelihoods. NPE trains an inference network to estimate a probability density over parameters given data, typically assumed to be…
Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…
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…
Defects are a universal feature of crystalline solids, dictating the key properties and performance of many functional materials. Given their crucial importance yet inherent difficulty in measuring experimentally, computational methods…
We introduce FDApy, an open-source Python package for the analysis of functional data. The package provides tools for the representation of (multivariate) functional data defined on different dimensional domains and for functional data that…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Meshing is a critical, but user-intensive process necessary for stable and accurate simulations in computational fluid dynamics (CFD). Mesh generation is often a bottleneck in CFD pipelines. Adaptive meshing techniques allow the mesh to be…
Accurate identification of chemical species and reaction pathways from molecular dynamics (MD) trajectories is a prerequisite for deriving predictive chemical-kinetic models and for mechanistic discovery in reactive systems. However,…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…