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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…
Nowadays, academic research relies not only on sharing with the academic community the scientific results obtained by research groups while studying certain phenomena, but also on sharing computer codes developed within the community. In…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
This tutorial provides a hands-on entry point about laser locking for atomic vapor research and related research such as laser cooling. We furthermore introduce common materials and methods for the fabrication of vapor cells as a tool for…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…
The detectors based on the liquid scintillator (LS) monitored by an array of photo-multiplier tubes (PMT) are often used in low energy experiments such as neutrino oscillation studies and search for dark matter. Detectors of this kind…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Computing systems are consuming an increasing and unsustainable fraction of society's energy footprint, notably in data centers. Meanwhile, energy-efficient software engineering techniques are often absent from undergraduate curricula. We…
Machine learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular…
We present ADAM, a software system for designing and running child language learning experiments in Python. The system uses a virtual world to simulate a grounded language acquisition process in which the language learner utilizes…
Cooling of beams circulating in storage rings is critical for many applications including particle colliders and synchrotron light sources. A method enabling unprecedented beam-cooling rates, optical stochastic cooling (OSC), was recently…
We analyze the dynamics of atom-laser interactions for atoms having multiple, closely spaced, excited-state hyperfine manifolds. The system is treated fully quantum mechanically, including the atom's center-of-mass degree of freedom, and…
Novel multiplexing triple-axis neutron scattering spectrometers yield significant improvements of the common triple-axis instruments. While the planar scattering geometry keeps ensuring compatibility with complex sample environments, a…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Asteroseismology is an exceptional tool for studying stars by using the properties of observed modes of oscillation. So far the process of performing an asteroseismic analysis of a star has remained somewhat esoteric and inaccessible to…
It has been roughly three decades since laser cooling techniques produced ultracold atoms, leading to rapid advances in a vast array of fields. Unfortunately laser cooling has not yet been extended to molecules because of their complex…
We report on the design, construction, and performance of a compact magnetic shield that facilitates a controlled, low-noise environment for experiments with ultracold atomic gases. The shield was designed to passively attenuate external…
This work describes extensions to existing level-set algorithms developed for application within the field of Atom Probe Tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level…
We present work flows and a software module for machine learning model building in surface science and heterogeneous catalysis. This includes fingerprinting atomic structures from 3D structure and/or connectivity information, it includes…