Related papers: i-PI: A Python interface for ab initio path integr…

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…

We present an introduction to the Quantum Toolbox in Python (QuTiP) in the context of an undergraduate quantum mechanics class and potential senior research projects. QuTiP provides ready-to-use definitions of standard quantum states and…

A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…

PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…

The shift in chemical equilibria due to isotope substitution is often exploited to gain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using…

Fluid-structure systems occur in a range of scientific and engineering applications. The immersed boundary(IB) method is a widely recognized and effective modeling paradigm for simulating fluid-structure interaction(FSI) in such systems,…

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond…

Ultracold atomic systems have been of great research interest in the past, with more recent attention being paid to systems of mixed species. In this work we carry out non-perturbative Path Integral Monte Carlo (PIMC) simulations of N…

We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…

The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…

Quasiparticle interference imaging (QPI) provides a route to characterize electronic structure from real space images acquired using scanning tunneling microscopy. It emerges due to scattering of electrons at defects in the material. The…

Trapped atomic ions are among the most advanced platforms for quantum simulation, computation, and metrology, offering long coherence times and precise, individual control over both internal and motional degrees of freedom. In this review,…

Accurate simulation of nuclear quantum effects is essential for molecular modeling but expensive using path integral molecular dynamics (PIMD). We present GG-PI, a ring-polymer-based framework that combines generative modeling of the…

Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…

Many modern and emerging applications must process increasingly large volumes of data. Unfortunately, prevalent computing paradigms are not designed to efficiently handle such large-scale data: the energy and performance costs to move this…

We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…

The small matrix path integral (SMatPI) method is an efficient numerical approach to simulate the evolution of a quantum system coupled to a harmonic bath. The method relies on a sequence of kernel matrices that defines the non-Markovian…

This paper introduces the design and implementation of PyOptInterface, a modeling language for mathematical optimization embedded in Python programming language. PyOptInterface uses lightweight and compact data structure to bridge…

We frame the issue of pedestrian dynamics modeling in terms of path-integrals, a formalism originally introduced in quantum mechanics to account for the behavior of quantum particles, later extended to quantum field theories and to…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…