Related papers: Advancing Scanning Probe Microscopy Simulations: A…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
A major challenge in Atomic Force Microscopy (AFM) is to reduce the scan duration while retaining the image quality. Conventionally, the scan rate is restricted to a sufficiently small value in order to ensure a desirable image quality as…
Microplastics (MPs) are ubiquitous in all ecosystems, affecting wildlife and, ultimately, human health. The complexity of natural samples plus the unspecificity of their treatments to isolate polymers renders the characterization of…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
Optical nanoscopy is crucial in life and materials sciences, revealing subtle cellular processes and nanomaterial properties. Scattering-type Scanning Near-field Optical Microscopy (s-SNOM) provides nanoscale resolution, relying on the…
Material properties such as permeability fields in heterogeneous porous media are often represented as discontinuous, piecewise constant data tied to a given spatial discretization. Such representations are inherently mesh-dependent,…
Plug-and-Play Priors (PnP) is one of the most widely-used frameworks for solving computational imaging problems through the integration of physical models and learned models. PnP leverages high-fidelity physical sensor models and powerful…
In the following article we develop a particle filter for approximating Feynman-Kac models with indicator potentials. Examples of such models include approximate Bayesian computation (ABC) posteriors associated with hidden Markov models…
Scattering-type scanning near-field optical microscopy (s-SNOM) is a powerful technique for extreme subwavelength imaging and spectroscopy, with around 20 nm spatial resolution. But quantitative relationships between experiment and material…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Multi-beam ptychography (MBP) offers a scalable solution to improve the throughput of state-of-the-art ptychography by increasing the number of coherent beams that illuminate the sample simultaneously. However, increasing the number of…
Atom probe tomography (APT) helps elucidate the link between the nanoscale chemical variations and physical properties, but it has limited structural resolution. Field ion microscopy (FIM), a predecessor technique to APT, is capable of…
Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…
Atomic Force Microscopy (AFM) allows to probe matter at atomic scale by measuring the perturbation of a nanomechanical oscillator induced by near-field interaction forces. The quest to improve sensitivity and resolution of AFM has forced…
Particle discretizations of partial differential equations are advantageous for high-dimensional kinetic models in phase space due to their better scalability than continuum approaches with respect to dimension. Complex processes…
Photoacoustic microscopy (PAM) has been a promising biomedical imaging technology in recent years. However, the point-by-point scanning mechanism results in low-speed imaging, which limits the application of PAM. Reducing sampling density…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Detector simulation and reconstruction are a significant computational bottleneck in particle physics. We develop Particle-flow Neural Assisted Simulations (Parnassus) to address this challenge. Our deep learning model takes as input a…