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We investigate the scattering and absorption of light by random ballistic aggregates of spherical monomers. We present a general measure for the porosity of an irregular particle. Three different classes of ballistic aggregates are…
The static-exchange model (SEM) and the modified static-exchange model (MSEM) recently introduced by Ray [1] is applied to study the elastic collision between two hydrogen-like atoms when both are in ground states considering the system as…
We propose a method using reduced size of Hilbert space to describe an electron dynamics in molecule and aggregate based on our previous theoretical scheme [ T. Yonehara and T. Nakajima, J. Chem. Phys. \textbf{147}, 074110 (2017) ]. The…
The electronic density of states (DOS) quantifies the distribution of the energy levels that can be occupied by electrons in a quasiparticle picture, and is central to modern electronic structure theory. It also underpins the computation…
Scanning transmission electron microscopy (STEM) has advanced rapidly in the last decade thanks to the ability to correct the major aberrations of the probe forming lens. Now atomic-sized beams are routine, even at accelerating voltages as…
A flux-splitting method is proposed for the hyperbolic-equation system (HES) of magnetized electron fluids in quasi-neutral plasmas. The numerical fluxes are split into four categories, which are computed by using an upwind method which…
The method of assessing porosity using images from scanning electron microscopy is ineffective in situations where the substrate and the coating have a significantly different average atomic number, which results in a different contrast of…
Conceiving a molecule as composed of smaller molecular fragments, or subunits, is one of the pillars of the chemical and physical sciences, and leads to productive methods in quantum chemistry. Using a fragmentation scheme, efficient…
A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…
Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the…
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in…
Context: There is increasing need for good algorithms for modeling the aggregation and fragmentation of solid particles (dust grains, dust aggregates, boulders) in various astrophysical settings, including protoplanetary disks, planetary-…
We consider Particle Gibbs (PG) as a tool for Bayesian analysis of non-linear non-Gaussian state-space models. PG is a Monte Carlo (MC) approximation of the standard Gibbs procedure which uses sequential MC (SMC) importance sampling inside…
The thorough treatment of electron-lattice interactions from first principles is one of the main goals in condensed matter physics. While the commonly applied adiabatic Born-Oppenheimer approximation is sufficient for describing many…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the…
We introduce the so called DeepParticle method to learn and generate invariant measures of stochastic dynamical systems with physical parameters based on data computed from an interacting particle method (IPM). We utilize the expressiveness…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
This publication presents an investigation of the performance of different analytical electron ptychography methods for low-dose imaging. In particular, benchmarking is performed for two model-objects, monolayer MoS$_2$ and apoferritin, by…
We describe recent progress in developing practical ab initio methods for which the computer effort is proportional to the number of atoms: linear scaling or O(N) methods. It is shown that the locality property of the density matrix gives a…