Improved CG force-field learning from all-atom data.
problem Training accurate coarse-grained models from all-atom simulations is challenging.
method Optimized force mapping to improve statistical efficiency of force-field learning.
result Substantially improved CG force-fields can be learned from the same simulation data.
New method uses normalizing flows to improve force fields for coarse-grained molecular dynamics.
problem Lack of reference atomistic forces makes force matching infeasible for MLCG force fields.
method Introduces noise-based kernels adapted to low-data regimes using normalizing flows.
result Flow-based kernels reduce local distortions while preserving global accuracy.
Machine learning generates coarse-grained force fields for molecular dynamics.
problem Creating thermodynamically consistent coarse-grained models for larger systems.
method Hybrid architecture using graph neural networks to learn molecular features.
result Framework reproduces thermodynamics for small biomolecular systems.
AniDS improves molecular force field modeling by learning anisotropic noise.
problem Molecular force field modeling suffers from oversimplified assumptions about atomic motions.
method AniDS introduces anisotropic noise generation for better modeling of directional and structural variability.
result AniDS outperforms existing methods on benchmarks, achieving significant improvements in force prediction accuracy.
BoostMD accelerates molecular dynamics simulations by 8x with ML force fields.
problem Long inference times of ML force fields limit practical use in molecular dynamics.
method BoostMD uses previous time-step features to predict energies and forces, reducing complexity and computational cost.
result BoostMD achieves an 8-fold speedup and accurately samples the Boltzmann distribution.
MACE architecture outperforms alternatives in various molecular and materials science tasks.
problem Improving machine learning force fields for diverse molecular and materials science applications.
method Evaluation of MACE architecture on various datasets and tasks, demonstrating data efficiency and excellent performance.
result MACE architecture generally outperforms alternatives across a wide range of systems, including amorphous carbon, universal materials modelling, and organic chemistry.
Paper improves molecular property prediction using denoising autoencoders.
problem Limited data for molecular property prediction from 3D structures.
method Pre-training via denoising for learning molecular force fields.
result Achieves new state-of-the-art performance on QM9 dataset.
GDML learns effective CG models from all-atom data.
problem Learning effective coarse-grained force fields efficiently.
method Ensemble learning with stratified sampling and GDML.
result GDML yields smaller free energy error than neural networks.
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 computations or the limited accuracy of classical empirical force fields. Machine l…
Proposes linking energy and force uncertainty in deep learning potentials.
problem Uncertainty in predicted energies and forces in machine learning models.
method Introduces a spatially correlated noise process to link energy and force uncertainty.
result Demonstrates the approach on molecular datasets, linking energy and force uncertainties.
New framework embeds physics in coarse-grained models without big data.
problem Lack of big data and computational demand in data-driven coarse-graining.
method Proposes a novel objective based on reverse Kullback-Leibler divergence that incorporates physics in the form of force fields.
result Generative coarse-grained model predicts atomistic configurations and reveals physicochemical CVs.
A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional conformation generation methods minimize hand-designed molecular force field energy functi…
A new method relaxes molecules without needing non-equilibrium data.
problem Molecular relaxation requires understanding non-equilibrium structures.
method MoreRed: molecular relaxation by reverse diffusion with time step prediction.
result MoreRed learns a simpler pseudo potential energy surface.
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such computationally expensive simulations is the definition of coarse-grained molecular models.…
ConfFlow uses transformer networks to generate molecular conformations efficiently.
problem Efficient generation of valid conformations for large molecules.
method Flow-based model using transformer networks that directly samples in coordinate space.
result ConfFlow improves accuracy by up to 40% for large molecule conformations.
Diffusion models simulate molecular dynamics with adjustable accuracy.
problem Simulating molecular dynamics with high accuracy and efficiency.
method Diffusion models as Euler-Maruyama integrators for Langevin dynamics, learning forces from static snapshots.
result Diffusion models generate molecular trajectories with temporal correlations similar to MD simulations.
Automates feature selection and weighting in molecular systems.
problem Optimal feature selection and alignment in molecular systems.
method Differentiable Information Imbalance (DII) method for automated feature ranking and scaling.
result Automated feature selection and scaling that preserves information content and interpretability.
LNK improves uncertainty estimation for molecular dynamics, reducing errors by up to 2.5 times.
problem Uncertainty estimation for molecular force fields to improve model reliability.
method LNK: Gaussian Process-based extension to GNNs addressing six desiderata.
result LNK reduces out-of-equilibrium detection errors by up to 2.5 times compared to existing methods.
Machine learning is used to approximate the kinetic energy of one dimensional diatomics as a functional of the electron density. The functional can accurately dissociate a diatomic, and can be systematically improved with training. Highly accurate self-consistent densities and molecular forces are found, indicating the…
The excited states of polyatomic systems are rather complex, and often exhibit meta-stable dynamical behaviors. Static analysis of reaction pathway often fails to sufficiently characterize excited state motions due to their highly non-equilibrium nature. Here, we proposed a time series guided clustering algorithm to ge…
Smooth flows for physical systems with smooth energies and forces.
problem Smooth energies for physical simulations and force computation.
method Smooth mixture transformations on compact intervals and hypertori, using root-finding and the inverse function theorem.
result Smooth flows allow training by force matching and use as molecular dynamics potentials.
Machine learning advances chemistry and materials science by enabling large-scale exploration of chemical space based on quantum chemical calculations. While these models supply fast and accurate predictions of atomistic chemical properties, they do not explicitly capture the electronic degrees of freedom of a molecule…
New algorithm efficiently trains machine learning models to atomic forces data.
problem Efficiently training machine learning models to large amounts of force data.
method Developed an efficient algorithm for training machine learning models to all available force data.
result Training to all available force data is only a few times more expensive than training to energies alone.
CG-BGs combine flow-based models with PMFs to sample large systems efficiently.
problem Sampling equilibrium molecular configurations from the Boltzmann distribution is challenging.
method Coarse-grained Boltzmann Generators (CG-BGs) use flow-based models and learned PMFs for efficient sampling.
result CG-BGs provide a practical route for sampling larger molecular systems efficiently.
Generative models accelerate molecular dynamics by four orders of magnitude.
problem Femtosecond time steps limit access to slow molecular processes.
method Deep generative modeling framework that accelerates sampling.
result Quantitative characterization of equilibrium ensembles and dynamical relaxation processes.
Equivariant networks improve geometric prediction without scalar approximations.
problem Efficiently predicting geometric tensors in real-world scenarios.
method Equivariant networks for geometric prediction.
result Equivariant networks can generalize to unseen systems for geometric prediction.
A new machine-learned CG model predicts protein structures efficiently.
problem Developing a universal, computationally efficient protein simulation model.
method Combining deep learning with all-atom protein simulations to create a transferable CG force field.
result The model predicts protein structures, intermediates, and fluctuations efficiently.
SchNarc combines SchNet and SHARC for efficient photodynamics simulations.
problem Efficiently simulate excited-state dynamics of complex molecules.
method Combines SchNet for multiple electronic states with SHARC for molecular dynamics, learning energies, forces, and couplings.
result Paves the way for efficient photodynamics simulations of complex systems.
Machine learning improves implicit solvent models for molecular dynamics.
problem Accurate modeling of solvent effects for biological molecules is challenging.
method Leveraging machine learning and multi-scale coarse graining, ISSNet models implicit solvent potentials.
result ISSNet models outperform traditional methods in reproducing protein thermodynamics.
Develops active learning for scale-bridging simulations.
problem Quantitative predictions in nanoporous media and inertial confinement fusion.
method Active learning approach to optimize fine-scale simulations for coarse-scale hydrodynamics.
result Optimizes use of fine-scale simulations for coarse-scale predictions.
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
problem Challenges in generating 3D molecules, especially in drug discovery and materials science.
method VecMol reimagines molecular representation by modeling 3D molecules as continuous vector fields over Euclidean space, parameterized by a neural field and generated using a latent diffusion model.
result Vector-field-based representations show promise for 3D molecular generation, validated on benchmarks.
Physics-informed machine learning models improve biomolecular system simulations.
problem Modeling unresolved interactions beyond classical force fields.
method Physics-informed neural networks and operator learning.
result Accurate, mechanistic, generalizable models for long-timescale kinetics.
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …
DenSNet learns electron densities for molecular dynamics, enabling accurate spectroscopic predictions.
problem Lack of accurate electronic observables in MLIPs for molecular dynamics.
method DenSNet uses SE(3)-equivariant neural networks to predict electron densities and total energy.
result DenSNet predicts infrared spectra with excellent agreement to experimental data.
Machine learning models simulate molecular spectra and reactions in solvents.
problem Accurate simulation of molecular spectra and reactions in solvent environments.
method Introduced FieldSchNet, a deep neural network for modeling molecular interactions with external fields.
result Demonstrated significant lowering of Claisen rearrangement reaction activation barrier using FieldSchNet.
Method learns molecular Hamiltonian for accurate electron dynamics predictions.
problem Predict electron dynamics in molecules using learned Hamiltonians.
method Combines linear statistical model with quantum Liouville equation time discretization.
result Predicted electron dynamics closely matches ground truth, even beyond training data.
Curve shortening flow shrinks curves to points under certain conditions.
problem Understanding how curves shrink under curve shortening flow with ambient forces.
method Rescaling and curvature bounds analysis following Gage and Hamilton.
result Curves shrink to round points under certain curvature conditions.
Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific, isolated biomedical properties. In this work, we propose a new cross-modal small mole…
New dataset abla2DFT for drug-like molecules benchmarks neural network potentials.
problem Lack of large, diverse datasets for training neural network potentials in quantum chemistry.
method Developed a new dataset abla2DFT containing energies, forces, and molecular properties for drug-like molecules. result First dataset with relaxation trajectories for drug-like molecules.
The paper finds that circles and logarithmic spirals are the only constant-speed ramps for a specific force field.
problem Determining planar curves for constant-speed motion under specific force conditions.
method Analyzing the motion of a particle under friction and a central force field.
result Every solution to the constant-speed motion problem approaches either a circle or a logarithmic spiral.
Energy-based diffusion models improve molecular sampling and simulation.
problem Inconsistency between diffusion model scores and equilibrium distributions.
method Fokker-Planck regularization to enforce consistency.
result Improved consistency and efficient sampling of biomolecular systems.
In this paper, we study the evolution of submannifold moving by mean curvature minus a external force field. We prove that the flow has a long-time smooth solution for all time under almost optimal conditions. Those conditions are that the second fundamental form on the initial submanifolds is not too large, the extern…
The paper establishes a connection between force-free fields and conformally geodesic fields.
problem Understanding the relationship between force-free fields and conformally geodesic fields.
method Developed an equivalence between force-free fields and conformally geodesic fields, generalized to arbitrary dimensions.
result Established that stationary points of hierarchies of L2 and L1-optimization problems are related by a conformal change of metric. Improved neural network models predict molecular and material properties efficiently.
problem Training neural networks for accurate interatomic potentials is computationally expensive.
method Gaussian moment-based neural networks with improved architecture and active learning.
result The new models achieve high accuracy and reduced training times.
Neural network models colloidal particle dynamics in non-equilibrium systems.
problem Analyzing non-equilibrium dynamics of many-body colloidal systems.
method Combining power functional theory and machine learning, training a neural network to predict internal force fields.
result The neural network accurately predicts dynamics in non-equilibrium systems, in good agreement with simulations.
New models suggest molecules that are often unfeasible to synthesize.
problem Models suggest molecules that are difficult to synthesize.
method Used a computer-aided synthesis planning program to analyze synthesizability of molecules generated by state-of-the-art models.
result State-of-the-art models generate molecules that are often unfeasible to synthesize.
The Giroux correspondence and the notion of a near force-free magnetic field are used to topologically characterize near force-free magnetic fields which describe a variety of physical processes, including plasma equilibrium. As a byproduct, the topological characterization of force-free magnetic fields associated with…
Machine learning aids excited-state molecular dynamics studies.
problem Challenges in studying electronically excited states of molecules.
method Employing machine learning techniques for excited-state molecular dynamics.
result Highlight successes and challenges in machine learning for excited-state processes.