Related papers: Ab initio Molecular Dynamics in Adaptive Coordinat…
Numerical simulations of relativistic plasmas have become more feasible, popular, and crucial for various astrophysical sources with the availability of computational resources. The necessity for high-accuracy particle dynamics is…
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…
For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with…
This article presents a new and efficient alternative to well established algorithms for molecular geometry optimization. The new approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate…
Atomic Force Microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule images the internal structure of molecules with an unprecedented resolution. The interpretation of these images is…
The large number of possible structures of metal-organic frameworks (MOFs) and their limitless potential applications has motivated molecular modelers and researchers to develop methods and models to efficiently assess MOF performance. Some…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
The rich information content of measurements in the molecular frame rather than the laboratory frame has motivated the development of several methods for aligning gas phase molecules in space. Even so, for asymmetric tops the problem of…
We propose a new method to characterize the spatial distribution of particles' vibrations in solids with much lower computational costs compared to the usual normal mode analysis. We excite the specific vibrational mode in a two dimensional…
We show how vibronic spectra in molecular systems can be simulated in an efficient and accurate way using first principles approaches without relying on the explicit use of multiple Born-Oppenheimer potential energy surfaces. We demonstrate…
Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In…
In order to find the equilibrium geometries of molecules and solids and to perform ab initio molecular dynamics, it is necessary to calculate the forces on the nuclei. We present a correlated sampling method to efficiently calculate…
Although the scientific principles of anthropogenic climate change are well-established, existing calculations of the warming effect of carbon dioxide rely on spectral absorption databases, which obscures the physical foundations of the…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
In this paper there is presented method for ab initio calculation of the phonon spectra. The method is based upon a direct calculation of the dynamical matrix via second derivatives of the total energy. The pseudopotential technique in…
We study the control by electromagnetic fields of molecular alignment and orientation, in a linear, rigid rotor model. With the help of a monotonically convergent algorithm, we find that the optimal field is in the microwave part of the…
We investigate the time evolution process of one selected (initially prepared by optical pumping) vibrational molecular state, coupled to all other intra-molecular vibrational states of the same molecule, and also to its environment.…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…