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PyCharge is a computational electrodynamics Python simulator that can calculate the electromagnetic fields and potentials generated by moving point charges and can self-consistently simulate dipoles modeled as Lorentz oscillators. To…
High-spatial-resolution vibrational spectroscopy is one of the principal techniques for nanoscale compositional analysis in biological materials. Here, we present a new method for the analysis of whole-cell biological specimens through…
Contemporary schemes for waveform-resolved characterization are constrained by setup-specific requirements, which severely limits their adaptability and fails to establish standard procedures for routine in-line diagnostic. This work…
The inelastic scattering of electrons is one route to study the vibrational and electronic properties of materials. Such experiments, also called electron energy-loss spectroscopy, are particularly useful for the investigation of the…
pySLAM is an open-source Python framework for Visual SLAM that supports monocular, stereo, and RGB-D camera inputs. It offers a flexible and modular interface, integrating a broad range of both classical and learning-based local features.…
The analysis of speech production based on physical models of the vocal folds and vocal tract is essential for studies on vocal-fold behavior and linguistic research. This paper proposes a speech production analysis method using…
The missing phase problem in X-ray crystallography is commonly solved using the technique of molecular replacement, which borrows phases from a previously solved homologous structure, and appends them to the measured Fourier magnitudes of…
Developing a deep understanding of macroscopic mechanical properties of amorphous systems which lack structural periodicity, has posed a key challenge, not only at the level of theory but also in molecular simulations. Despite significant…
Transmission electron microscopes use electrons with wavelengths of a few picometers, potentially capable of imaging individual atoms in solids at a resolution ultimately set by the intrinsic size of an atom. Unfortunately, due to…
We introduce the first, general purpose, slice sampling inference engine for probabilistic programs. This engine is released as part of StocPy, a new Turing-Complete probabilistic programming language, available as a Python library. We…
Electron spin resonance (ESR) pulsed dipolar spectroscopy (PDS) is used effectively in measuring nano-meter range distances for protein structure prediction. The current global approach in extracting the distance distribution from time…
Analytical electron microscopy and spectroscopy of biological specimens, polymers, and other beam sensitive materials has been a challenging area due to irradiation damage. There is a pressing need to develop novel imaging and spectroscopic…
The knowledge of the local electronic structure of heterogeneous solid materials is crucial for understanding their electronic, magnetic, transport, optical, and other properties. VASP, one of the mostly used packages for density-functional…
The sound-localization and, in particular, biosonar system of toothed whales is exceptionally performant. How this is achieved is not clear, given that: (i) toothed whales have no pinnae; (ii) while their auditory pathways have been studied…
Automated molecular simulations are used extensively for predicting material properties. Typically, these simulations exhibit two regimes: a dynamic equilibration part, followed by a steady state. For extracting observable properties, the…
Magnonics is seen nowadays as a candidate technology for energy-efficient data processing in classical and quantum systems. Pronounced nonlinearity, anisotropy of dispersion relations and phase degree of freedom of spin waves require…
The Liouville-Lanczos approach to linear-response time-dependent density-functional theory is generalized so as to encompass electron energy-loss and inelastic X-ray scattering spectroscopies in periodic solids. The computation of virtual…
Elasticity is one of the most fundamental mechanical properties of solid. In high-throughput design of advanced materials, there is an imperative demand for the capability to quickly calculate and screen a massive pool of candidate…
Starting from the observation that one of the most successful methods for solving the Kohn-Sham equations for periodic systems -- the plane-wave method -- is a spectral method based on eigenfunction expansion, we formulate a spectral method…
While multislice electron ptychography can provide thermal-vibration limited resolution and 3D information, it relies on the proper selection of many intertwined experimental and computational parameters. Here, we outline a theoretical…