Related papers: A Bayesian approach for extracting free energy pro…
Electron microscopy has enabled many scientific breakthroughs across multiple fields. A key challenge is the tuning of microscope parameters based on images to overcome optical aberrations that deteriorate image quality. This calibration…
Free energy of crystal phases is commonly evaluated by thermodynamic integration (TDI) along a reversible path that involves an external potential. A persistent problem in this method is that a significant hysteresis is observed due to…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…
Host-guest interactions govern the chemistry of a broad range of functional materials. However, the weak bonding between host and guest prevents atomic-resolution studies of their structure and chemistry using transmission electron…
Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET…
Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
Particle picking is currently a critical step in the cryo-electron microscopy single particle reconstruction pipeline. Contaminations in the acquired micrographs severely degrade the performance of particle pickers, resulting is many…
Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a…
Motivated by the problem of determining the atomic structure of macromolecules using single-particle cryo-electron microscopy (cryo-EM), we study the sample and computational complexities of the sparse multi-reference alignment (MRA) model:…
Modern microscopy techniques are aimed at imaging an individual molecule at atomic resolution. Here we show that low-energy electrons with kinetic energies of 50-250 eV offer a possibility of overcome the problem of radiation damage, and…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
The growing role of data-driven approaches to scientific discovery has unveiled a large class of models that involve latent transformations with a rigid algebraic constraint. Three-dimensional molecule reconstruction in Cryo-Electron…
Single-Particle Reconstruction (SPR) in Cryo-Electron Microscopy (cryo-EM) is the task of estimating the 3D structure of a molecule from a set of noisy 2D projections, taken from unknown viewing directions. Many algorithms for SPR start…
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for resolving the three-dimensional structures of macromolecules. A key challenge in cryo-EM is characterizing continuous heterogeneity, where molecules adopt a…
Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation…
Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the…