Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-1394-8_14 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
High-Throughput Exploration of Ti-V-Nb-Mo Carbide MXenes Using Neural Network Potentials and Their Evaluation as Catalysts for Hydrogen Evolution Reaction.
ACS Appl Mater Interfaces
December 2024
TCS Research, Sahyadri Park 2, Rajiv Gandhi Infotech Park, Hinjewadi Phase 3, Pune 411057, India.
Realization of a sustainable hydrogen economy in the future requires the development of efficient and cost-effective catalysts for its production at scale. MXenes (MX) are a class of 2D materials with 'n' layers of carbon or nitrogen (X) interleaved by 'n+1' layers of transition metal (M) and have emerged as promising materials for various applications including catalysts for hydrogen evolution reaction (HER). Their properties are intimately related to both their composition and their atomic structure.
View Article and Find Full Text PDFQuantitative Live Imaging Reveals Phase Dependency of PDAC Patient-Derived Organoids on ERK and AMPK Activity.
Cancer Sci
December 2024
Department of Molecular Oncology, Graduate School of Medicine, Osaka University, Osaka, Japan.
Patient-derived organoids represent a novel platform to recapitulate the cancer cells in the patient tissue. While cancer heterogeneity has been extensively studied by a number of omics approaches, little is known about the spatiotemporal kinase activity dynamics. Here we applied a live imaging approach to organoids derived from 10 pancreatic ductal adenocarcinoma (PDAC) patients to comprehensively understand their heterogeneous growth potential and drug responses.
View Article and Find Full Text PDFCancer Organoids as reliable disease models to drive clinical development of novel therapies.
J Exp Clin Cancer Res
December 2024
Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
On September 23-24 (2024) the 6th Workshop IRE on Translational Oncology, titled "Cancer Organoids as Reliable Disease Models to Drive Clinical Development of Novel Therapies," took place at the IRCCS Regina Elena Cancer Institute in Rome. This prominent international conference focused on tumor organoids, bringing together leading experts from around the world.A central challenge in precision oncology is modeling the dynamic tumor ecosystem, which encompasses numerous elements that evolve spatially and temporally.
View Article and Find Full Text PDFMultiplexed amplicon sequencing reveals the heterogeneous spatial distribution of pyrethroid resistance mutations in Aedes albopictus mosquito populations in southern France.
Parasit Vectors
December 2024
Institut de Recherche Biomédicale des Armées (IRBA), Unité de Parasitologie et Entomologie, Marseille, France.
Background: The risk of mosquito-borne disease transmission is increasing in temperate climates with the colonization and proliferation of the Asian tiger mosquito vector Aedes albopictus and the rapid mass transport of passengers returning from tropical regions where viruses are endemic. The prevention of major Aedes-borne viruses heavily relies on the use of insecticides for vector control, mainly pyrethroids. In Europe, only deltamethrin is authorized.
View Article and Find Full Text PDFTransposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response.
Nat Struct Mol Biol
December 2024
Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
Infectious diseases drive wild plant evolution and impact crop yield. Plants, like animals, sense biotic threats through pattern recognition receptors (PRRs). Overly robust immune responses can harm plants; thus, understanding the tuning of defense response mechanisms is crucial for developing pathogen-resistant crops.
View Article and Find Full Text PDFWant 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!