Related papers: Extension of the simulation code ACAT to treat rea…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…
The Automated Contact Angle Tester (ACAT) is a fully integrated robotic work cell developed to automate the measurement of surface wettability on 3D-printed materials. Designed for precision, repeatability, and safety, ACAT addresses the…
In this thesis, we introduce a novel formal framework to represent and reason about qualitative direction and distance relations between extended objects using Answer Set Programming (ASP). We take Cardinal Directional Calculus (CDC) as a…
Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B connected via a linker C. The existing ISAPT algorithm displays…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
Quantum computation and quantum simulation require a versatile gate set to optimize circuit compilation for practical applications. However, existing platforms are often limited to specific gate types or rely on parametric couplers to…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Communication in the presence of bounded timing asynchronism which is known to the receiver but cannot be easily compensated is studied. Examples of such situations include point-to-point communication over inter-symbol interference (ISI)…
Advancements in computing based on qubit networks, and in particular the flux-qubit processor architecture developed by D-Wave System's Inc., have enabled the physical simulation of quantum-dot cellular automata (QCA) networks beyond the…
Simulating charge and energy transfer in extended molecular networks requires an effective model to include the environment because it significantly affects the quantum dynamics. A prototypical effect known as Environment-Assisted Quantum…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…
Molecular Nanomagnets may enable the implementation of qudit-based quantum error-correction codes which exploit the many spin levels naturally embedded in a single molecule, a promising step towards scalable quantum processors. To fully…
Channel simulation algorithms can efficiently encode random samples from a prescribed target distribution $Q$ and find applications in machine learning-based lossy data compression. However, algorithms that encode exact samples usually have…
Electromagnetic scattering and absorption by material particles is a fundamental physical problem with a broad range of applications, going from laboratory experiments, biology and material sciences, all the way up to environmental studies…