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This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…
Simulations, although powerful in accurately replicating real-world systems, often remain inaccessible to non-technical users due to their complexity. Conversely, large language models (LLMs) provide intuitive, language-based interactions…
Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…
The detection and classification of intersections between triangles are crucial tasks in a wide range of applications within Computer Graphics and Geometry Processing, including mesh Arrangements, mesh Booleans, and generic mesh processing…
Process simulation is a critical cornerstone of chemical engineering design. Current automated chemical design methodologies focus mainly on various representations of process flow diagrams. However, transforming these diagrams into…
Structurally and chemically complex materials such as amorphous metallosilicates underpin major catalytic and separation technologies, yet their intrinsic complexity challenges reliable atomistic modeling under realistic conditions.…
This paper presents our approach to use refactoring techniques together with code generation. Refactoring is particularly useful if not only the generated classes but also the generator itself can be adapted in an automatic fashion. We have…
We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified software interface. Our framework is intrinsically parallel, and conveniently separates all components in memory. It…
Quantum circuits are time dependent diagrams describing the process of quantum computation. Usually, a quantum algorithm must be mapped into a quantum circuit. Optimal synthesis of quantum circuits is intractable and heuristic methods must…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
We develop a general method for incentive-based programming of hybrid quantum-classical computing systems using reinforcement learning, and apply this to solve combinatorial optimization problems on both simulated and real gate-based…
Simulation offers a simple and flexible way to estimate the power of a clinical trial when analytic formulae are not available. The computational burden of using simulation has, however, restricted its application to only the simplest of…
In this paper, we propose and evaluate the performance of a unified computational framework for preconditioning systems of linear equations resulting from the solution of coupled problems with monolithic schemes. The framework is composed…
A modular, maintainable and extensible particle beam simulation architecture is presented. Design considerations for single particle, multi particle, and rms envelope simulations (in two and three dimensions) are outlined. Envelope…
Modelling of multivariate densities is a core component in many signal processing, pattern recognition and machine learning applications. The modelling is often done via Gaussian mixture models (GMMs), which use computationally expensive…
Trilinos is a community-developed, open-source software framework that facilitates building large-scale, complex, multiscale, multiphysics simulation code bases for scientific and engineering problems. Since the Trilinos framework has…
We introduce a constraint-based framework for studying infinite qualitative simulations concerned with contingencies such as time, space, shape, size, abstracted into a finite set of qualitative relations. To define the simulations, we…
Quantum simulation, the simulation of quantum processes on quantum computers, suggests a path forward for the efficient simulation of problems in condensed-matter physics, quantum chemistry, and materials science. While the majority of…
This paper consists of three parts. The first part provides a unified programming model for heterogeneous computing with CPU and accelerator (like GPU, FPGA, Google TPU, Atos QPU, and more) technologies. To some extent, this new programming…