Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a 'black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557182PMC
http://dx.doi.org/10.1107/S1600576719004333DOI Listing

Publication Analysis

Top Keywords

molecular dynamics
20
classical molecular
12
dynamics simulation
8
dynamics simulations
8
molecular
5
dynamics
5
scattering
5
introduction classical
4
simulation experimental
4
experimental scattering
4

Similar Publications

Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm.

View Article and Find Full Text PDF

Al-air batteries are distinguished by their high theoretical energy density, yet their broader application is hindered by hydrogen evolution corrosion. This research focuses Beta (+) d-glucose (S1) and Adonite (S2) as potential corrosion inhibitors for the Al-5052 alloy within a 4 M NaOH solution. Utilizing electrochemical techniques, hydrogen evolution assessments, and surface analyses, our findings indicate enhancements in anode utilization by 21.

View Article and Find Full Text PDF

Understanding the spatial and temporal dynamics of gene expression is crucial for unraveling molecular mechanisms underlying various biological processes. While traditional methods have offered insights into gene expression patterns, they primarily focus on mature mRNA transcripts, lacking real-time visualization of newly synthesized or nascent transcription events. Recent advancements in monitoring nascent transcription in live cells provide valuable insights into transcriptional dynamics.

View Article and Find Full Text PDF

Circular RNAs in the pathogenesis of SARS-CoV-2: potential diagnostic biomarkers and therapeutic targets.

Funct Integr Genomics

January 2025

Department of Clinical Laboratory, the Fourth Affiliated Hospital of School of medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.

Since December 2019, the global dissemination of a novel coronavirus has precipitated a notable public health crisis, prompting considerable interest and scrutiny from governmental and scholarly entities. Substantial research efforts have been dedicated to exploring diverse facets of this novel coronavirus, encompassing its pathogenesis, transmission dynamics, and therapeutic interventions. Recent findings suggest that circular RNAs (circRNAs) exert a pivotal influence on modulating viral infectivity and immune defense mechanisms.

View Article and Find Full Text PDF

αβT cells protect vertebrates against many diseases, optimizing surveillance using mechanical force to distinguish between pathophysiologic cellular alterations and normal self-constituents. The multi-subunit αβT-cell receptor (TCR) operates outside of thermal equilibrium, harvesting energy via physical forces generated by T-cell motility and actin-myosin machinery. When a peptide-bound major histocompatibility complex molecule (pMHC) on an antigen presenting cell is ligated, the αβTCR on the T cell leverages force to form a catch bond, prolonging bond lifetime, and enhancing antigen discrimination.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!