Generative machine learning is increasingly used for inorganic crystal structure generation. Most models and the corresponding evaluation approaches rely on simple forms of crystal structure represent...

Since lipid bilayers are self-assembled macroscopic aggregates, their constituent lipid molecules can spontaneously transition between the two leaflets. This so

Nanoparticles are promising drug carriers for targeted therapies, diagnostic imaging, and advanced vaccines. However, their clinical translation is limited by c

Machine-learned force fields are becoming increasingly popular but suffer from their “black-box” nature. Here the authors adapt explainable AI techniques to coarse-grained graph neural network potenti...

Argyrodite-type Ag-based sulfides combine exceptionally low lattice thermal and high ionic conductivity, making them promising candidates for thermoelectric and solid-state energy applications. In thi...

Who invented convolutional neural networks?

A popular heuristic derived from the Kanamori-Goodenough-Anderson rules of superexchange connects bond angles and magnetism in certain transition metal compounds. We evaluate the fulfillment of this h...

The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...

Material discovery is a cornerstone of modern science, driving advancements in diverse disciplines from biomedical technology to climate solutions. Predicting synthesizability, a critical factor in re...

FIORA, an advanced graph neural network, enhances the simulation of tandem mass spectra by learning molecular bond-breaking patterns. The open-source algorithm generates high-quality reference spectra...

We introduce the Velocity Jumps approach, denoted as JUMP, a new class of Molecular dynamics integrators, replacing the Langevin dynamics by a hybrid model combining a classical Langevin diffusion and a piecewise deterministic Markov process, where the expensive computation of long-range pairwise interactions is replaced by a resampling of the velocities at random times. This framework allows for an acceleration in the simulation speed while preserving sampling and dynamical properties such as the diffusion constant. It can also be integrated in classical multi-time-step methods, pushing further the computational speedup, while avoiding some of the resonance issues of the latter thanks to the random nature of jumps. The JUMP, JUMP-RESPA and JUMP-RESPA1 integrators have been implemented in the GPU-accelerated version of the Tinker-HP package and are shown to provide significantly enhanced performances compared to their BAOAB, BAOAB-RESPA and BAOAB-RESPA1 counterparts, respectively.

During neurotransmission, presynaptic action potentials trigger synaptic vesicle fusion with the plasma membrane within milliseconds. To visualize membrane dynamics before, during, and right after ves...

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simula...

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles. - drorlab/pensa

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

A key property of reasoning systems is the ability to make sharp decisions on their input data. For contemporary AI systems, a key carrier of sharp behaviour is the softmax function, with its capabili...

The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond time scale. For long time steps, the numerical integration of the equations of m...

The field of data-driven chemistry is undergoing an evolution, driven by innovations in machine learning models for predicting molecular properties and behavior. Recent strides in ML-based interatomic...