Related papers: A Bayesian approach for extracting free energy pro…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…
We present a parameter-free method of extraction of the electron magnetic circular dichroism spectra from energy-filtered diffraction patterns measured on crystalline specimen. The method is based on multivariate curve resolution technique.…
In this paper, we present a novel Bayesian approach for estimating spectral and range profiles from single-photon Lidar waveforms associated with single surfaces in the photon-limited regime. In contrast to classical multispectral Lidar…
Finding optimal solutions to combinatorial optimization problems is pivotal in both scientific and technological domains, within academic research and industrial applications. A considerable amount of effort has been invested in the…
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to…
We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to…
Quantitative high-resolution transmission electron microscopy (HRTEM) provides an indispensable means to understand the structure-property relationships of a material in atomic dimensions. Successful quantification requires reliable…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a…
Modern microscopy techniques are developing towards high-resolution imaging, and tremendous progress has been made in past decades; however, the imaging of individual biological macromolecules at atomic resolution using short-wavelength…
A novel approach is proposed, where energy filtered electrons, carrying both chemical identity and electrical information, serve as fine and flexible electrodes in direct electrical measurements. The method, termed 'chemically resolved…
Multi-Energy Computed Tomography (ME-CT) is a medical imaging modality aiming to reconstruct the spatial density of materials from the attenuation properties of probing x-rays. For each line in two- or three-dimensional space, ME-CT…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
Microcanonical thermostatistics analysis has become an important tool to reveal essential aspects of phase transitions in complex systems. An efficient way to estimate the microcanonical inverse temperature $\beta(E)$ and the microcanonical…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
Cryo-electron microscopy (cryoEM) is an increasingly popular method for protein structure determination. However, identifying a sufficient number of particles for analysis (often >100,000) can take months of manual effort. Current…