Related papers: RepEx: A Flexible Framework for Scalable Replica E…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support…
We propose a class of subspace ascent methods for computing optimal approximate designs that covers both existing as well as new and more efficient algorithms. Within this class of methods, we construct a simple, randomized exchange…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Existing prompt-optimization techniques rely on local signals to update behavior, often neglecting broader and recurring patterns across tasks, leading to poor generalization; they further rely on full-prompt rewrites or unstructured…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
Simulation experiments are typically conducted repeatedly during the model development process, for example, to re-validate if a behavioral property still holds after several model changes. Approaches for automatically reusing and…
Exascale systems, expected to emerge by the end of the next decade, will require the exploitation of billion-way parallelism at multiple hierarchical levels in order to achieve the desired sustained performance. The task of assessing future…
In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…
In an era where we can not afford to checkpoint frequently, replication is a generic way forward to construct numerical simulations that can continue to run even if hardware parts fail. Yet, replication often is not employed on larger…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
Compute Express Link (CXL) serves as a rising industry standard, delivering high-speed cache-coherent links to a variety of devices, including host CPUs, computational accelerators, and memory devices. It is designed to promote system…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
In today's Web and social network environments, query workloads include ad hoc and OLAP queries, as well as iterative algorithms that analyze data relationships (e.g., link analysis, clustering, learning). Modern DBMSs support ad hoc and…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…