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As we reach exascale, production High Performance Computing (HPC) systems are increasing in complexity. These systems now comprise multiple heterogeneous computing components (CPUs and GPUs) utilized through diverse, often vendor-specific…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
The growing complexity of Cyber-Physical Systems (CPS), together with increasingly available parallelism provided by multi-core chips, fosters the parallelization of simulation. Simulation speed-ups are expected from co-simulation and…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Model predictive control (MPC) combined with reduced-order template models has emerged as a powerful tool for trajectory optimization in dynamic legged locomotion. However, loco-manipulation tasks performed by legged robots introduce…
GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…
To match the growing demand for bio-methane production, anaerobic digesters need to embrace the co-digestion of different feedstocks; in addition, to improve the techno-economic performance, an optimal and time-varying adaptation of the…
Gaussian Processes (GPs) are flexible, nonparametric Bayesian models widely used for regression and classification because of their ability to capture complex data patterns and quantify predictive uncertainty. However, the O(n^3)…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
Nonlinear Model Predictive Control (NMPC) is a powerful approach for controlling highly dynamic robotic systems, as it accounts for system dynamics and optimizes control inputs at each step. However, its high computational complexity makes…
Writing high-performance image processing code is challenging and labor-intensive. The Halide programming language simplifies this task by decoupling high-level algorithms from "schedules" which optimize their implementation. However, even…
The modular open-source framework GRAMPC-D for model predictive control of distributed systems is presented in this paper. The modular concept allows to solve optimal control problems (OCP) in a centralized and distributed fashion using the…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Hierarchical $\mathcal{H}^2$-matrices are asymptotically optimal representations for the discretizations of non-local operators such as those arising in integral equations or from kernel functions. Their $O(N)$ complexity in both memory and…
PYROBOCOP is a Python-based package for control, optimization and estimation of robotic systems described by nonlinear Differential Algebraic Equations (DAEs). In particular, the package can handle systems with contacts that are described…
We address the challenge of adopting language models (LMs) for embodied tasks in dynamic environments, where online access to large-scale inference engines or symbolic planners is constrained due to latency, connectivity, and resource…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…