Publications by authors named "A Y Nesterenko"
Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the structure and dynamics of biomembranes with atomic resolution. The validity of the representations obtained is determined by the accuracy and realism of the MD model (force field). Here, we evaluated the proprietary OPLS4 force field of Schrödinger, Inc.
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- Embryonic scaling is a unique biological phenomenon where embryos adjust their spatial structure according to their size, initially described in sea urchins.
- Recent research has aimed to understand the role of specific genes, termed "scalers," which are crucial in regulating morphogen concentration gradients in correlation with embryo size.
- The findings confirm that scalers, including the gene Mmp3, exist in various reaction-diffusion system models and play a vital role in maintaining gradient scaling across different embryonic types.
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes.
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- During gastrulation and neurulation in vertebrate embryos, the chordamesoderm and neuroectoderm converge and extend under a genetic program.
- This study investigates whether mechanical tension from these movements influences gene expression in these tissues.
- By analyzing stretched midgastrula embryo explants, researchers found that mechanical stretching activates certain genes in the stretched trunk region while inhibiting others in low-stretch areas, suggesting that mechanical forces could regulate embryonic patterning and development.
Ferroptosis is a type of programmed cell death distinct from apoptosis and necroptosis that plays an essential role in pathophysiological conditions such as neurodegenerative diseases and tumorigenesis. Massive lipid oxidation in an iron-dependent manner is a hallmark of ferroptosis.This modality of cell death is also characterized by perturbation of several metabolic pathways, predominantly fatty acid metabolism, thiol metabolism, iron homeostasis and the mevalonate pathway.
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