simulation

Discovery of Natural MCL1 Inhibitors using Pharmacophore modelling, QSAR, Docking, ADMET, Molecular Dynamics, and DFT Analysis

The paper identifies two potential MCL1 inhibitors through computational methods including pharmacophore modeling, QSAR, docking, and DFT analysis, showing favorable ADMET properties and binding stability.

Tresor: An integrated platform for simulating transcriptomic reads with realistic PCR error representation across various RNA sequencing technologies

Tresor simulates transcriptomic reads with PCR error representation across sequencing technologies, showing cell-type-specific profiles similar to reference data after duplicate removal.

Investigating the topological motifs of inversions in pangenome graphs

The paper investigates inversion topological motifs in pangenome graphs and finds significant variation in inversion representation across pipelines, with poor recovery in real human data.

Aggregation and disaggregation of red blood cells: depletion versus bridging

This study investigates RBC aggregation and disaggregation mechanisms using simulations, finding depletion interactions dominate aggregation while both mechanisms contribute to disaggregation.

Buffer specificity of ionizable lipid nanoparticle transfection efficiency and bulk phase transition

This study investigates how buffer type affects lipid nanoparticle structure and transfection efficiency, finding citrate buffer enhances mRNA expression through altered phase transitions.

Biofilm-derived polymer networks constrain immune cell motility through adhesion-mediated physical interactions

This study shows that biofilm exopolysaccharides impede macrophage motility and directional persistence, using microfluidic models and simulations.

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

Two Tetrahymena ribozyme cryo-EM maps (2.2 and 2.3 Å) reveal cross-validated ordered waters and Mg2+ ions, plus reproducible diffuse solvent density resembling molecular dynamics water networks.

Network topology creates independent control of G2-M from G1-S checkpoints in the fission yeast cell cycle system

The paper uses a topology-based theory to predict and validate independent control of G2-M and G1-S checkpoints in fission yeast cell cycle by analyzing CDK-cyclin complex dynamics.

Individual-Based Modeling of Microbial Communities Integrating Genetic Mechanisms: A Case Study of LuxS-Mediated Quorum Sensing in Salmonella Typhimurium

The paper presents a digital twin framework for simulating microbial communities at the single-cell level, integrating genetic mechanisms to study quorum sensing and virulence in Salmonella Typhimurium.

The "very moment" when UDG recognizes aflipped-out uracil base in dsDNA

This study uses molecular dynamics simulations to show that DNA mechanics can induce base-flipping, facilitating UDG recognition of uracil bases in chromatin.

In silico nanoscope to study the interplay of genome organization and transcription regulation

The paper develops a multiscale modeling pipeline to simulate chromatin organization and transcription regulation in mouse embryonic stem cells, revealing how sequence-regulated accessibility facilitates enhancer-promoter communication.

vcfgl: A flexible genotype likelihood simulator for VCF/BCF files

vcfgl simulates genotype likelihoods to study uncertainties and biases in genetic data, aiding in benchmarking GL-based methods.

Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer

This study shows that horizontal gene transfer promotes alternative stable states in microbial communities through various mechanisms.

MOSim: bulk and single-cell multi-layer regulatory network simulator

MOSim generates synthetic bulk and single-cell multi-omics datasets for benchmarking methods that analyze regulatory networks across various omics layers.

Using an agent based model to inform sampling design for animal social network analysis

The paper uses an agent-based model to evaluate how sampling strategies affect the accuracy of social network metrics in animal studies, identifying optimal trade-offs between coverage, frequency, and duration.

A teneurin-3 microphthalmia mutation disrupts trans adhesion for specific alternative splicing isoforms

The paper shows that a mutation in teneurin-3 disrupts trans adhesion specifically in splice isoforms containing insert A, contributing to microphthalmia.

Dynamically rich states in balanced networks induced by single-neuron dynamics

The paper shows that weak synaptic coupling and intrinsic cellular dynamics can generate rich network states with enhanced variability and information encoding in balanced networks.

A comparative assessment of self-limiting genetic control strategies for population suppression

This study compares self-limiting genetic control strategies for pest population suppression using simulations, finding some are safer, more flexible, and cost-effective than traditional methods.

Spatial dynamics and emergent properties of pLS20 conjugation on solid surfaces

This study uses hybrid modeling to show spatial organization and quorum-sensing regulation significantly influence plasmid dissemination during bacterial conjugation on solid surfaces.

Unraveling the distinct motion bias of TrkA-NGF complex in NGFR100W-driven HSAN V disease

This study uses molecular dynamics simulations to analyze how NGFR100W mutation affects the structural dynamics of the TrkA-NGF complex, revealing altered motion patterns linked to HSAN V disease mechanisms.

Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories

The paper benchmarks ARG estimation methods for their performance in estimating population-mean polygenic score histories using simulated data.

Phylogenetic discordance can substantially overestimate genomic reassortment in avian influenza virus

The paper shows that phylogenetic discordance can overestimate reassortment in avian influenza viruses due to reconstruction errors and suggests methods to reduce false positives.

An Experimental and Multiphysics Simulations Study of Clostridium carboxidivorans sp. 624 for Acid and Alcohol Production in CO2/H2

This study optimizes CO2/H2 fermentation by Clostridium carboxidivorans sp. 624 using experimental and computational methods to enhance acid production.

Information transmission in a cell monolayer: A numerical study

The paper uses a numerical model to study information transmission in cell monolayers, identifying stochastic factors that affect wave propagation and determining optimal channel widths and wave frequencies for effective communication.

AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow

AsaruSim simulates synthetic single-cell Nanopore long-read datasets to evaluate isoform detection methods using human PBMC data.

Mathematical modelling predicts novel mechanisms of stream confinement from Trail/Colec12/Dan in the collective migration of cranial neural crest cells

The paper uses an agent-based model to simulate how Trail, Colec12, and Dan confine cranial neural crest cells to stereotypical migration pathways in vivo.

Managing the genetic diversity of animal populations using cryobanks: optimizing the constitution of ex situ collection?

This study optimizes the constitution of cryopreserved collections for managing genetic diversity in animal populations by simulating breeding scenarios and evaluating the impact of collection size, age, and sampling strategies.

Apical-driven cell sorting optimised for tissue geometry ensures robust patterning

The paper shows apical polarity in PrE cells drives robust tissue patterning in blastocysts by guiding migration and breaking symmetry.

Dynamic Disorder in Chlorophyll Aggregation and Light-Harvesting Complex II in the Plant Thylakoid Membrane using Coarse-Grained Simulations

This study uses coarse-grained simulations to investigate dynamic disorder in chlorophyll aggregation and LHCII conformations in plant thylakoid membranes, revealing non-exponential decay and multiple time scales in dimer formation and inter-CLA fluctuations.

SEEDS: Simulating Emergence of Errors in DNA Storage

SEEDS simulates error accumulation in DNA storage pipelines and validates it against experimental data to evaluate error correction schemes.