arXiv subjects

Ivet Bahar

Publications and source records attributed to Ivet Bahar.

4 recordsLinked to original sources

arXiv2025

The need to implement FAIR principles in biomolecular simulations

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/) Now published as: Amaro, R.E., et al. The need to implement FAIR principles in biomolecular simulations. Nat Methods (2025) https://doi.org/10.1038/s41592-025-02635-0

q-bio.BM↗

arXiv2011

Stochastic modeling of p53-regulated apoptosis upon radiation damage

We develop and study the evolution of a model of radiation induced apoptosis in cells using stochastic simulations, and identified key protein targets for effective mitigation of radiation damage. We identified several key proteins associated with cellular apoptosis using an extensive literature survey. In particular, we focus on the p53 transcription dependent and p53 transcription independent pathways for mitochondrial apoptosis. Our model reproduces known p53 oscillations following radiation damage. The key, experimentally testable hypotheses that we generate are - inhibition of PUMA is an effective strategy for mitigation of radiation damage if the treatment is administered immediately, at later stages following radiation damage, inhibition of tBid is more effective.

physics.bio-ph↗

arXiv2011

Biomolecular transitions: efficient computation of pathways, free energies, and rates

We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure divides the configurational space into smaller regions and equilibrates trajectories within each region efficiently. The equilibrated conditional probabilities between each pair of regions lead to transition rates between the two states. We apply the procedure to a non-trivial coarse-grained model of a 70 residue section of the calcium binding protein, calmodulin. The procedure yields a significant increase in efficiency compared to brute-force simulations, and this efficiency increases dramatically with a decrease in temperature.

physics.bio-ph↗

arXiv2006

Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae

BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the context of the cell's own internal state. However, the network topological basis of developing such integrated responses remains poorly understood. RESULTS. By studying the TR network of the yeast Saccharomyces cerevisiae we show that an intermediate layer of transcription factors naturally segregates into distinct subnetworks. In these topological units transcription factors are densely interlinked in a largely hierarchical manner and respond to external signals by utilizing a fraction of these subnets. CONCLUSIONS. As transcriptional regulation represents the "slow" component of overall information processing, the identified topology suggests a model in which successive waves of transcriptional regulation originating from distinct fractions of the TR network control robust integrated responses to complex stimuli.

q-bio.MN↗