simulation

Therapeutic Relevance of NLPA Lipoprotein to Combat Biofilm-Associated infection in Acinetobacter baumannii

The paper identifies two compounds targeting NLPA, a lipoprotein involved in biofilm formation in Acinetobacter baumannii, showing antibacterial and biofilm inhibition activity in vitro and reduced intracellular survival in macrophages.

From 3D Time-of-Flight Angiography to Accelerated 4D Arterial Spin Labeling Angiography: A Fast Few-Shot Transfer Learning Approach

This paper develops a fast few-shot transfer learning approach for reconstructing highly accelerated 4D arterial spin labeling angiography using simulated data and minimal experimental data.

Elevated conformational dynamics makes ACKR3 activation-prone and G protein-incompetent

This study compares the conformational dynamics of ACKR3 and CXCR4 using MD simulations and BRET assays, revealing that ACKR3's dynamic behavior leads to activation-proneness and G protein-incompetence.

Biocosm: A Simulation Environment for Designing Energy-Constrained Ethological Sensors

This paper introduces a simulation framework for energy-constrained ethological sensors to evaluate how sensing policies affect data collection and behavioral inference.

From time-course expression to gene regulation: direct linear ODE inference without finite-difference approximation

Fitting a linear ODE with an equilibrium term via its matrix-exponential solution, not finite differences, raises TF-network AUROC over competing methods on simulated and scRNA-seq data.

Multi-site temporal control of optogenetic stimulation enhances firing frequencies in peripheral nerves

This study shows that multi-site optogenetic stimulation can increase firing rates in peripheral nerves through in silico, ex vivo, and in vivo experiments.

Report on pre-validation of an animal-free alternative method (NAM) for regulatory safety testing: InfiniteLungDT, an in-vitro-learned digital twin for the prediction of material-triggered chronic neutrophilic lung inflammation

The paper pre-validates an animal-free method, InfiniteLungDT, which predicts chronic neutrophilic lung inflammation using in vitro data, achieving high accuracy in LOAEL determination.

INTEGRATOR: Structural Elucidation of the INO80 Chromatin Remodeler via Experimentally Guided Molecular Simulations

The paper presents a computational model of the S. cerevisiae INO80 chromatin remodeling complex using integrative methods, revealing the structure and dynamics of key modules and introducing the INTEGRATOR workflow tool.

Can leptin-specific epigenetic modulation of preterm cord blood predispose obesity?

The paper examines if leptin promoter methylation in preterm cord blood is associated with adiposity and inflammation in neonates.

simCRISPR: Modeling experimental complexity in pooled CRISPR screens

The paper develops simCRISPR, a simulation framework for pooled CRISPR screens, evaluates normalization strategies for detecting gene-by-environment interactions, and shows improved results with safe-harbor normalization.

Dendrite-soma interactions in cultured hippocampal neurons form non-random structural motifs with local presynaptic enrichment and strengthening

The paper identifies non-random structural motifs in dendrite-soma interactions in cultured hippocampal neurons and shows their association with presynaptic enrichment and strengthening.

A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics

The paper shows how tissue rigidity phase transitions and Nodal morphogen gradients interact to drive patterning dynamics in zebrafish.

Towards harmonized spectral quantification in MRSI: Comparative analysis of Backward-Linear-Predicted and original 1H-FID-MRSI dephased data

The paper compares Backward-Linear-Prediction (BLP) and original 1H-FID-MRSI data to assess quantification biases caused by acquisition delay and shows BLP improves consistency across different delays.

Large-domain histology-based diffusion MRI simulation via independent local simulations

This paper develops a framework to simulate diffusion MRI from histology at clinically relevant scales, showing accurate results with reduced computational cost.

Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking

This study evaluates enhanced sampling methods for RNA force field benchmarking using an 8-mer tetraloop, finding T-REMD most robust for accurate folding free energy estimates.

Computer experimentation on E. coli ammonium transport and assimilation reveals mechanisms for energy coupling, balanced futile cycling, and robust growth

The paper compares kinetic models of E. coli ammonium transport and assimilation to determine the mechanism of energy coupling and growth robustness under varying conditions.

A Comprehensive Benchmarking of Spatial Deconvolution andDomain Detection Methods across Diverse Tissues and SpatialTranscriptomic Technologies

This paper benchmarks spatial deconvolution and domain detection methods across diverse tissues and technologies, identifying top-performing approaches and highlighting method limitations.

When can neuronal activity-dependent homeostatic plasticity maintain circuit-level properties?

The paper investigates how activity-dependent homeostatic plasticity can maintain circuit-level properties in a computational model of the pyloric circuit.

tugMedi: simulator of cancer-cell evolution for personalized medicine based on the genomic data of patients

tugMedi simulates cancer-cell evolution using patient genomic data to predict drug responses and tumor dynamics.

Hearts may grow concentrically to balance ATP supply and demand and eccentrically to stabilize titin-based stress

This paper uses simulations to show that concentric and eccentric cardiac growth are regulated by ATP homeostasis and titin-based stress, respectively, and can model growth patterns from both genetic and clinical causes.

MucOneUp: A Simulation Framework for MUC1-VNTR Variant Benchmarking

MucOneUp generates MUC1-VNTR reference sequences and simulated sequencing reads to benchmark variant calling tools across platforms.

Photoreceptor outer segment disk rim curvature relies on a tetraspanin interaction web

This study investigates the structural role of PRPH2 and Rom1 in photoreceptor outer segment disk curvature using BN-PAGE and MD simulations, revealing their interaction web and curvature mechanisms.

A computational model reveals that spatial localization of cancer stem cells increases radioresistance in tumorspheres

This paper shows that cancer stem cells in tumorspheres are more radioresistant due to their spatial localization in hypoxic regions, which protects them from radiation.

From lab to ocean: bridging swimming energetics and wild movements to understand red drum (Sciaenops ocellatus) behavior in a tidal estuary

Red drum lowered oxygen consumption behind mangrove- and oyster-mimicking bluff bodies at flows to 100 cm/s, yet telemetered fish were detected mostly in low-velocity nearshore habitat.

Goals as dynamical attractors: a momentum-based account of stable and flexible goal commitment

This study proposes a momentum-based framework for understanding goal commitment, showing how dynamic attractors balance stability and flexibility in goal pursuit through simulations and behavioral analysis.

Few-shot learning of predictive features with dendrites and behavioural timescale synaptic plasticity in the hippocampus

The paper proposes a model of hippocampal pyramidal neurons that use predictive learning through dendritic compartments and synaptic plasticity to encode spatial and behaviorally relevant features.

Efficient Stochastic Trace Generation for Transcription

The paper introduces a unified SDE framework for efficient stochastic transcription trace generation, showing high accuracy with reduced computational cost.

Evolution imposes an inductive bias that alters and accelerates learning dynamics

This study shows evolutionarily conditioned neural networks exhibit unique learning dynamics and can be rapidly fine-tuned, suggesting evolution provides an inductive bias for efficient learning.

REDUCED-PRECISION STOCHASTIC SIMULATION FOR MATHEMATICAL BIOLOGY

This paper evaluates reduced-precision floating-point arithmetic for accelerating stochastic simulations in mathematical biology without compromising statistical accuracy.

Biodistribution of mRNA vaccines in rats: Enrichment in injection site and lymph tissues and rapid clearance without tissue persistence

Three mRNA-LNP products sharing one lipid matrix show rat intramuscular biodistribution (injection site, lymph nodes, spleen) and rapid clearance, with no Spike accumulation after repeat dosing.