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Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
We introduce a new image contrast mechanism for scanning transmission electron microscopy (STEM) that derives from the local symmetry within the specimen. For a given position of the electron probe on the specimen, the image intensity is…
We present an efficient \textit{ab initio} algorithm for quantum dynamics simulations of interacting systems that is based on the conditional decomposition of the many-body wavefunction [Phys. Rev. Lett. 113, 083003 (2014)]. Starting with…
Collision detection plays a key role in the simulation of interacting rigid bodies. However, owing to its computational complexity current methods typically prioritize either maximizing processing speed or fidelity to real-world behaviors.…
We present a new annotated microscopic cellular image dataset to improve the effectiveness of machine learning methods for cellular image analysis. Cell counting is an important step in cell analysis. Typically, domain experts manually…
In this study, we apply the monitoring master equation describing decoherence of internal states to an optically active molecule prepared in a coherent superposition of nondegenerate internal states interacting with thermal photons at low…
Optical coherence tomography (OCT) is capable of non-destructively obtaining cross-sectional information of samples with micrometer spatial resolution, which plays an important role in ophthalmology and endovascular medicine. Measuring OCT…
We investigate image segmentation of cells under the lens of scalar fields. Our goal is to learn a continuous scalar field on image domains such that its segmentation produces robust instances for cells present in images. This field is a…
Large high-dimensional datasets are becoming more and more popular in an increasing number of research areas. Processing the high dimensional data incurs a high computational cost and is inherently inefficient since many of the values that…
We outline a modeling and optimization strategy for investigating dynamic metabolic engineering interventions. Our framework is particularly useful at the early stages of research and development, often constrained by limited knowledge and…
We investigate molecular dynamics of multiple ionization in N2 through multiple core-level photoabsorption and subsequent Auger decay processes induced by intense, short X-ray free electron laser pulses. The timing dynamics of the…
Spectral molecular imaging is a new imaging technique able to discriminate and quantify different components of tissue simultaneously at high spatial and high energy resolution. Our MARS scanner is an x-ray based small animal CT system…
The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the x-ray damage effects observed in x-ray scattering measurements of biological and chemical materials, as well…
Pump-probe microscopy of melanin in tumors has been proposed to improve diagnosis of malignant melanoma, based on the hypothesis that aggressive cancers disaggregate melanin structure. However, measured signals of melanin are complex…
The soft character of organic materials leads to strong coupling between molecular nuclear and electronic dynamics. This coupling opens the way to control charge transport in organic electronic devices by inducing molecular vibrational…
We present a finite difference time domain (FDTD) model for computation of A line scans in time domain optical coherence tomography (OCT). By simulating only the end of the two arms of the interferometer and computing the interference…
Recent advances in techniques for monitoring and perturbing neural populations have greatly enhanced our ability to study circuits in the brain. In particular, two-photon holographic optogenetics now enables precise photostimulation of…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…
Optical coherence tomography (OCT) has proven to be a powerful technique for studying tissue morphology in ophthalmology, cardiology, and endomicroscopy. Its performance is limited by the fundamental trade-off between the imaging…
Modern time series are usually composed of multiple oscillatory components, with time-varying frequency and amplitude contaminated by noise. The signal processing mission is further challenged if each component has an oscillatory pattern,…