Related papers: DynamO: A free O(N) general event-driven molecular…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found,…
We introduce an algorithm to compute Hamiltonian dynamics on digital quantum computers that requires only a finite circuit depth to reach an arbitrary precision, i.e. achieves zero discretization error with finite depth. This finite number…
Real-world applications are now processing big-data sets, often bottlenecked by the data movement between the compute units and the main memory. Near-memory computing (NMC), a modern data-centric computational paradigm, can alleviate these…
Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…
Visual Simultaneous Localization and Mapping (V-SLAM) methods achieve remarkable performance in static environments, but face challenges in dynamic scenes where moving objects severely affect their core modules. To avoid this, dynamic…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
Open quantum many-body systems are of both fundamental and applicational interest. However, it remains an open challenge to simulate and solve such systems, both with state-of-the-art classical methods and with quantum-simulation protocols.…
We present a quantum algorithm that analyzes time series data simulated by a quantum differential equation solver. The proposed algorithm is a quantum version of the dynamic mode decomposition algorithm used in diverse fields such as fluid…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
The design of optimization algorithms for neural networks remains a critical challenge, with most existing methods relying on heuristic adaptations of gradient-based approaches. This paper introduces KO (Kinetics-inspired Optimizer), a…
Quantum computing offers promising new avenues for tackling the long-standing challenge of simulating the quantum dynamics of complex chemical systems, particularly open quantum systems coupled to external baths. However, simulating such…
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
Neural operators, which aim to approximate mappings between infinite-dimensional function spaces, have been widely applied in the simulation and prediction of physical systems. However, the limited representational capacity of network…
We describe a major update to the public GIZMO code. GIZMO has been used in simulations of cosmology; galaxy and star formation and evolution; black hole accretion and feedback; proto-stellar disk dynamics and planet formation; fluid…