Related papers: MiMiC: A High-Performance Framework for Multiscale…
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates…
MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we…
Computational models have become one of the prevalent methods to model complex phenomena. To accurately model complex interactions, such as detailed biomolecular interactions, scientists often rely on multiscale models comprised of several…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Task-based programming models have become very popular, as they offer an attractive solution to parallelize serial application code with task and data annotations. They usually depend on a runtime system that schedules the tasks to multiple…
Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present…
In this paper is proposed a technique to integrate and simulate a dynamic memory in a multiprocessor framework based on C/C++/SystemC. Using host machine's memory management capabilities, dynamic data processing is supported without…
We present MISTIQS, a Multiplatform Software for Time-dependent Quantum Simulations. MISTIQS delivers end-to-end functionality for simulating the quantum many-body dynamics of systems governed by time-dependent Heisenberg Hamiltonians…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
This work introduces MICSim, an open-source, pre-circuit simulator designed for early-stage evaluation of chip-level software performance and hardware overhead of mixed-signal compute-in-memory (CIM) accelerators. MICSim features a modular…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
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,…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
NISQ devices have several physical limitations and unavoidable noisy quantum operations, and only small circuits can be executed on a quantum machine to get reliable results. This leads to the quantum hardware under-utilization issue. Here,…