Related papers: Conformations of Macromolecules and their Complexe…
Mapping conformational heterogeneity of macromolecules presents a formidable challenge to X-ray crystallography and cryo-electron microscopy, which often presume its absence. This has severely limited our knowledge of the conformations…
Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
Macromolecules change their shape (conformation) in the process of carrying out their functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of macromolecules (single particles) is a powerful and general…
The field of cryo-electron microscopy has made astounding advancements in the past few years, mainly due to advancements in electron detectors' technology. Yet, one of the key open challenges of the field remains the processing of…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a…
Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…
In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…
In complex plasmas, the behavior of freely floating micrometer sized particles is studied. The particles can be directly visualized and recorded by digital video cameras. To analyze the dynamics of single particles, reliable algorithms are…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
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…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and…
Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…
An algorithm for the computation of global discrete conformal parametrizations with prescribed global holonomy signatures for triangle meshes was recently described in [Campen and Zorin 2017]. In this paper we provide a detailed analysis of…
Microheterogeneity, as a fundamental natural property, is widely presented in a range of microscopic systems such as polymer systems, biomacromolecular systems, and nanosystems, however, the construction of molecular systems of this form…
One of the difficulties in 3D reconstruction of molecules from images in single particle Cryo-Electron Microscopy (Cryo-EM), in addition to high levels of noise and unknown image orientations, is heterogeneity in samples: in many cases, the…
Proteins and other macromolecules exist not in a single state but as dynamic ensembles of interconverting conformations, which are essential for catalysis, allosteric regulation, and molecular recognition. While AI-based structure…