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Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been…
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
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…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
Denoising generative models, such as diffusion and flow-based models, produce high-quality samples but require many denoising steps due to discretization error. Flow maps, which estimate the average velocity between timesteps, mitigate this…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
An accurate modeling of reactive flows in fractured porous media is a key ingredient to obtain reliable numerical simulations of several industrial and environmental applications. For some values of the physical parameters we can observe…
Reconstructing high-quality magnetic resonance images (MRI) from undersampled raw data is of great interest from both technical and clinical point of views. To this date, however, it is still a mathematically and computationally challenging…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Rectified flow models have become a de facto standard in image generation due to their stable sampling trajectories and high-fidelity outputs. Despite their strong generative capabilities, they face critical limitations in image editing…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
Although many deep-learning-based super-resolution approaches have been proposed in recent years, because no ground truth is available in the inference stage, few can quantify the errors and uncertainties of the super-resolved results. For…
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular…
In image restoration, single-step discriminative mappings often lack fine details via expectation learning, whereas generative paradigms suffer from inefficient multi-step sampling and noise-residual coupling. To address this dilemma, we…