Related papers: ExTASY: Scalable and Flexible Coupling of MD Simul…
The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named Exploratory…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
The transition from petascale to exascale computers is characterized by substantial changes in the computer architectures and technologies. The research community relying on computational simulations is being forced to revisit the…
This study presents a novel workflow for constructing hybrid macropore-Darcy models from micro-CT images of microporous rocks. In our approach, macropore networks are extracted using established methods, while the microporosity is…
Scientific discovery increasingly requires executing heterogeneous scientific workflows on high-performance computing (HPC) platforms. Heterogeneous workflows contain different types of tasks (e.g., simulation, analysis, and learning) that…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
There are many science applications that require scalable task-level parallelism and support for flexible execution and coupling of ensembles of simulations. Most high-performance system software and middleware, however, are designed to…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
Diffusion and flow-matching have emerged as powerful methodologies for generative modeling, with remarkable success in capturing complex data distributions and enabling flexible guidance at inference time. Many downstream applications,…
The constrained nature of synthesizable chemical space poses a significant challenge for sampling molecules that are both synthetically accessible and possess desired properties. In this work, we present PrexSyn, an efficient and…
Slice Sampling has emerged as a powerful Markov Chain Monte Carlo algorithm that adapts to the characteristics of the target distribution with minimal hand-tuning. However, Slice Sampling's performance is highly sensitive to the…
Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe time-scale limitations. To address this, enhanced sampling methods have been developed to improve exploration of…
Diffusion models (DMs) have established themselves as the state-of-the-art generative modeling approach in the visual domain and beyond. A crucial drawback of DMs is their slow sampling speed, relying on many sequential function evaluations…
As part of the EU-funded Center of Excellence SPACE (Scalable Parallel Astrophysical Codes for Exascale), seven commonly used astrophysics simulation codes are being optimized to exploit exascale computing platforms. Exascale cosmological…
Realistic simulations in engineering or in the materials sciences can consume enormous computing resources and thus require the use of massively parallel supercomputers. The probability of a failure increases both with the runtime and with…
Visual analytics is arguably the most important step in getting acquainted with your data. This is especially the case for time series, as this data type is hard to describe and cannot be fully understood when using for example summary…
Exa-scale simulations are on the horizon but almost no new design for the output has been proposed in recent years. In simulations using individual time steps, the traditional snapshots are over resolving particles/cells with large time…
Recent masked diffusion models (MDMs) have shown competitive performance compared to autoregressive models (ARMs) for language modeling. While most literature has focused on performance enhancing sampling procedures, efficient sampling from…
Massive upgrades to science infrastructure are driving data velocities upwards while stimulating adoption of increasingly data-intensive analytics. While next-generation exascale supercomputers promise strong support for I/O-intensive…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…