Atomic Scale Dynamics
Atomic Scale Dynamics - Related Videos
04:56
High-Speed Time-Lapse Atomic Force Microscopy to Capture Nucleosome Dynamics
0 Views •
2025
In this video, we demonstrate high-speed time-lapse atomic force microscopy, AFM, imaging techniques to study the dynamics of nucleosome complexes. As the AFM tip scans across the surface of the nucleosome, it detects alterations in the nucleosome height and records the DNA unwrapping over time.
02:30
In Vitro Culturing Technique for Studying Cellular Dynamics in Zebrafish Scales
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2025
This protocol offers a method to study cellular dynamics using a simple in vitro culture technique. It provides an opportunity for zebrafish researchers and educators to study cellular processes, such as those related to bone homeostasis and basic cell biology, by visualizing fluorescent nuclei and apoptotic cells within the scales.
14:55
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Cited by 3 •
2017
Structures of supramolecular protein assemblies at atomic resolution are of high relevance because of their crucial roles in a variety of biological phenomena. Herein, we present a protocol to perform high-resolution structural studies on insoluble and non-crystalline macromolecular protein assemblies by magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS SSNMR).
10:22
Studying Muscle Transcriptional Dynamics at Single-molecule Scales in Drosophila
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Cited by 3 •
2023
Drosophila is a well-established model for studying key molecules that regulate myogenesis. However, current methods are insufficient to determine mRNA transcriptional dynamics and spatial distribution within syncytia. To address this limitation, we optimized an RNA fluorescence in situ hybridization method allowing the detection and quantification of mRNAs at a single-molecule scale.
09:17
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Cited by 2 •
2022
The goal of this protocol is to reveal structural dynamics of one-dimensional diffusion of protein along DNA, using a plant transcription factor WRKY domain protein as an exemplary system. To do this, both atomistic and coarse-grained molecular dynamics simulations along with extensive computational samplings have been implemented.
FAQs
Interatomic forces determine how atoms interact, while thermal energy supplies the energy needed for vibration, diffusion, and rearrangement. Their balance influences whether atoms remain near preferred positions or move into new local configurations. In engineering materials, this balance helps explain why structural changes occur under different conditions and how those changes affect material behavior.
Atomic motion can appear differently depending on the length and time scale being examined. Small-scale observations reveal changes in neighboring atoms, bonding, and local structure, while longer or broader observations can show diffusion, defect development, or phase transformation. Matching the analysis scale to the process helps connect atomic behavior with measurable engineering performance.
Changes in atomic positions, bonding, and local structure can indicate that a material is rearranging rather than simply vibrating around an existing configuration. These changes provide evidence of processes such as defect formation, diffusion, or phase transformation. Interpreting them together helps distinguish temporary atomic motion from changes that alter the material’s structure and response.
An investigation can track how atomic positions, bonding, and local structure change over time. The resulting patterns are interpreted in relation to characteristic length and time scales, thermal energy, and interatomic forces. This approach connects microscopic motion with processes such as diffusion, defect development, phase transformation, mechanical response, or material degradation.
Atomic-scale analysis can clarify how defects form, how atoms diffuse, and how phases transform. It also supports interpretation of mechanical response and material degradation by linking those outcomes to changes in atomic positions and local structure. These insights help engineers identify the microscopic processes that influence performance, durability, and structural reliability.
Understanding atomic motion helps engineers relate local structural changes to material strength, durability, and degradation. By examining how bonding, defects, diffusion, and phase transformations contribute to material response, researchers can better control structures at the nanoscale. The same perspective also supports improved control of devices and systems whose performance depends on nanoscale organization.