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.
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.
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.…
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.
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 provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomis…
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 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.
New CGMD model predicts non-equilibrium processes better than existing methods.
problem Inconsistency in conditional distribution of unresolved variables.
method Time-lagged independent component analysis to minimize entropy contribution of unresolved variables.
result The model's generalization ability for non-equilibrium processes is significantly improved.
Graph neural network predicts optimal coarse-grained mapping operators.
problem Optimal coarse-grained mapping operators selection for molecular dynamics simulations.
method Graph Neural Network (DSGPM) trained on expert-annotated data.
result DSGPM outperforms state-of-the-art methods in graph segmentation.
DiAMoNDBack models protein backmapping from coarse-grained Cα traces.
problem Restoring all-atom details from coarse-grained protein representations.
method Autoregressive denoising diffusion model for residue-by-residue backmapping.
result Achieves state-of-the-art reconstruction performance in diverse applications.
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.
LSS learns molecular trajectories from MD data.
problem Limited integration time steps in MD simulations.
method Three deep learning networks for slow collective variables, dynamics, and configuration reconstruction.
result Generates ultra-long synthetic folding trajectories.
Introduce a thermodynamically informed, temperature-transferable MLCG framework for proteins.
problem Temperature transferability of MLCG models for proteins.
method Explicit decomposition of CG potential into energetic and entropic components.
result Reproduces temperature-dependent quantities like heat capacity.
Framework learns surrogates for molecular dynamics across multiple time-scales.
problem Stable molecular dynamics simulations require small time-steps, but long-time-scale moments need repeated simulations.
method Implicit Transfer Operator Learning with denoising diffusion probabilistic models and SE(3) equivariant architecture.
result Models can generate self-consistent stochastic dynamics across multiple time-scales.
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.
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown, and thus models built on the detailed, mechanistic viewpoint overfit and are not …
New CVs preserve transition rates in molecular dynamics.
problem Designing CVs that accurately capture rare events in high-dimensional systems.
method Integrating manifold learning and group-invariant featurization to construct neural network-based CVs that satisfy orthogonality conditions.
result Achieved a CV for butane that reproduces the anti-gauche transition rate with less than ten percent relative error.
Statistical (machine learning) tools for equation discovery require large amounts of data that are typically computer generated rather than experimentally observed. Multiscale modeling and stochastic simulations are two areas where learning on simulated data can lead to such discovery. In both, the data are generated w…
We derive a data-driven method for the approximation of the Koopman generator called gEDMD, which can be regarded as a straightforward extension of EDMD (extended dynamic mode decomposition). This approach is applicable to deterministic and stochastic dynamical systems. It can be used for computing eigenvalues, eigenfu…
Riemannian geometry improves protein dynamics analysis.
problem Efficient analysis of protein dynamics data in non-linear spaces.
method Developed a local approximation technique for geodesics and a smooth manifold of protein conformations.
result Geodesics approximate molecular dynamics trajectories and provide realistic summary statistics.
ISOKANN learns collective variables and effective dynamics for metastable transitions.
problem Understanding metastable transitions in complex molecular systems.
method Integrates Koopman operators with neural networks to extract CVs and effective dynamics.
result Reconstructs coarse-grained kinetics and reproduces transition times across barriers.
Framework preserves emergent physics in non-equilibrium systems from particle trajectories.
problem Linking short spatiotemporal scales to emergent bulk physics in multiscale systems.
method Metriplectic bracket formalism for structure-preserving coarse-graining.
result Preservation of thermodynamic laws and conservation in machine-learned dynamics.
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.
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical interest is computationally infeasible or impractical. In complex systems, with lim…
Temporal coarse-graining of latent default paths explains effective correlation in corporate defaults.
problem Understanding effective default correlation in corporate defaults.
method Temporal coarse-graining of latent default-probability paths, applied to corporate default-count data.
result Temporal coarse-graining provides a scale-consistent baseline that improves identifiability and reduces over-allocation of long-horizon fluctuations.
This study uses persistent homology to analyze complex transitional networks from time series data.
problem Lack of effective tools to summarize complex topology in transitional networks.
method Persistent homology from topological data analysis applied to coarse-grained state-space networks (CGSSN).
result CGSSN improves dynamic state detection and noise robustness compared to other methods.
New couplings improve understanding of molecular dynamics convergence.
problem Understanding convergence of Andersen dynamics in high dimensions.
method Presented couplings to obtain sharp convergence bounds in the Wasserstein sense.
result Sharp convergence bounds in the Wasserstein sense without global convexity.
WSINDy identifies reduced Hamiltonian systems from particle interactions.
problem Coarse-graining Hamiltonian dynamics with approximate symmetries.
method WSINDy algorithm applied to Hamiltonian systems with timescale separation.
result WSINDy successfully identifies reduced Hamiltonian systems from noisy data.
Timewarp accelerates molecular dynamics by learning to simulate long timescales.
problem Efficiently simulating long timescales in molecular dynamics.
method Uses a normalizing flow to learn large time steps in Markov chain Monte Carlo.
result Generalizes to unseen small peptides, accelerating sampling.
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.
Temporal aggregation reveals latent default correlation from monthly data.
problem Understanding effective default correlation from monthly default data.
method Temporal coarse-graining of latent default-probability paths.
result Temporal coarse-graining improves identifiability and reduces over-allocation of long-horizon fluctuations.
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…
Novel graph network learns hierarchical network structure.
problem Lack of information in hierarchical network topology.
method Hierarchical clustering for multiscale decomposition, graph convolutional layers.
result Competitive performance on citation network benchmark.
RC flow learns molecular kinetics in low dimensions.
problem Discovering interpretable low-dimensional models of molecular kinetics.
method Normalizing flow for coordinate transformation and Brownian dynamics for kinetics approximation.
result Tractable and trainable model of reduced kinetics in continuous time and space.
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a data-based, probablistic perspective that enables the quantification of predictive u…
Generative framework learns effective, lower-dimensional models from high-dimensional data.
problem Predicting long-term behavior of complex, multiscale systems with limited data.
method Physics-aware probabilistic model order reduction with latent variables.
result Guaranteed long-term stability and predictive accuracy in multiscale physical systems.
The paper develops a physics-aware method for modeling multiscale dynamics with reduced data.
problem Discovering effective, lower-dimensional models for high-dimensional dynamical systems.
method Probabilistic deep neural networks incorporating physical constraints.
result The method reduces the need for extensive multiscale simulations (Small Data regime).
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.
New methods use machine learning to simulate rare transitions in molecular systems.
problem Simulating rare transitions between metastable states in molecular dynamics.
method Generative models and reinforcement learning for importance sampling.
result Efficiently generated transition paths linking metastable states.
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.
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.
RNN operators solve Newton's equations with large timesteps for molecular dynamics.
problem Solving Newton's equations of motion with large timesteps for molecular dynamics simulations.
method Recurrent Neural Networks (RNN) operators to solve Newton's equations using past trajectory data.
result Significant speedup in molecular dynamics simulations with timesteps up to 4000 times larger.
A machine learning model captures non-Newtonian fluid dynamics from molecular details.
problem Creating accurate non-Newtonian fluid models from molecular data.
method Developed a machine learning framework that maps micro-scale polymer configurations to macro-scale fluid dynamics, preserving molecular fidelity.
result The deep non-Newtonian model (DeePN2) accurately predicts fluid behavior without empirical closures. The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow collective motions governing the long-time conformational dynamics of a system. It is challenging to intuit these slow CVs for all but the simpl…
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.
Temporal coarse-graining of multi-sector default count data generates effective correlation matrices and rank copulas.
problem Explaining the difference in default dependence between monthly and annual aggregation.
method Dynamic low-rank state-space model with AR(1) latent credit-state factors.
result Effective correlation matrices and rank copulas are generated from monthly default count data.
This review explores the use of machine learning in discovering collective variables for biomolecular dynamics.
problem Understanding the conformational dynamics and molecular recognition in biomolecules.
method Statistical analysis of high-dimensional spatiotemporal data generated from molecular dynamics simulations.
result Machine learning algorithms can be used to discover abstract collective variables that describe biomolecular dynamics.