Related papers: The CP-PAW code package for first-principles calcu…
We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and…
Modification of coupled integral equations method (CIEM) for calculating the characteristics of the accelerating structures is presented in this paper. In earlier developed CIEM schemes the coupled integral equations are derived for the…
Quantum simulators, in which well controlled quantum systems are used to reproduce the dynamics of less understood ones, have the potential to explore physics that is inaccessible to modeling with classical computers. However, checking the…
We apply a dynamical systems approach to concatenation of quantum error correcting codes, extending and generalizing the results of Rahn et al. [1] to both diagonal and nondiagonal channels. Our point of view is global: instead of focusing…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
We demonstrate the feasibility of quantum computing for large-scale, realistic chemical systems through the development of a new interface using a quantum circuit simulator and CP2K, a highly efficient first-principles calculation software.…
Condensed-phase spectral line shapes encode the strength and timescale of interactions between molecules and their environments, yet these ideas are often difficult to introduce at the undergraduate level due to their reliance on formal…
Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…
The CP-PACS Project, which started in April 1992, is a five-year plan to develop a massively parallel computer for carrying out research in computational physics with primary emphasis on lattice QCD. This article describes the architectural…
Cyber-physical systems (CPSs) embed software into the physical world. They appear in a wide range of applications such as smart grids, robotics, intelligent manufacture and medical monitoring. CPSs have proved resistant to modeling due to…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
An open-source, Python-based Temporal Analysis of Products (TAP) reactor simulation and processing program is introduced. TAPsolver utilizes algorithmic differentiation for the calculation of highly accurate derivatives, which are used to…
In computer simulations, quantum delocalization of atomic nuclei can be modeled making use of the Path Integral (PI) formulation of quantum statistical mechanics. This approach, however, comes with a large computational cost. By restricting…
This article introduces the pammtools package, which facilitates data transformation, estimation and interpretation of Piece-wise exponential Additive Mixed Models. A special focus is on time-varying effects and cumulative effects of…
yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Vibrational spectra of condensed and gas-phase systems containing light nuclei are influenced by their quantum-mechanical behaviour. The quantum dynamics of light nuclei can be approximated by the imaginary time path integral (PI)…
Computing maximum a posteriori (MAP) estimation in graphical models is an important inference problem with many applications. We present message-passing algorithms for quadratic programming (QP) formulations of MAP estimation for pairwise…