simulation

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation

The paper presents a large-scale biophysically detailed model of somatosensory cortex to simulate and validate cortical dynamics and experimental results.

De novo protein ligand design including protein flexibility and conformational adaptation

This paper introduces AI-MCLig, a method for designing protein ligands that accounts for protein flexibility and conformational adaptation, achieving binding scores comparable to known binders.

Engineering Cybergenetic Cell-Based Therapies

This paper develops a control-theoretic framework for engineering closed-loop cell-based therapies using nullgram profiling and a digital twin platform to achieve robust regulation of cellular behavior.

CATERPillar: A Flexible Framework for Generating White Matter Numerical Substrates with incorporated Glial Cells

CATERPillar generates realistic white matter numerical substrates with axons and glial cells, validated against histology and diffusion models.

Controlling Payload Heterogeneity in Lipid Nanoparticles for RNA-Based Therapeutics

This study identifies the causes of payload heterogeneity in lipid nanoparticles and proposes methods to improve RNA distribution uniformity.

MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery

MaAsLin 3 fits hurdle models separating microbial prevalence (augmented logistic) and abundance (median-adjusted log-linear) associations, improving precision over existing differential abundance tools and showing 77% of IBD associations are prevalence-driven.

Design-of-Experiments for Nonlinear, Multivariate Biology: Rethinking Experimental Design through Perturb-seq

The paper evaluates experimental design in Perturb-seq, finding that correlated designs are robust in systems with signal amplification and introduces a metric to predict optimal designs.

Sequence constraints predispose Class D GPCRs to follow an atypical activation mechanism

This study identifies sequence constraints that predispose Class D GPCRs to an atypical activation mechanism involving TM7 displacement and TM6 inward movement.

CCAN forms the spherical shell-like structure in interphase kinetochores

The paper shows that CCAN forms a spherical shell-like structure in interphase kinetochores using in silico and in vivo analyses.

Haemodynamic impact of implant materials and anastomotic angle in peripheral vascular grafts

This study uses fluid-structure interaction simulations to evaluate how graft material, suture material, and anastomosis angle affect blood flow and shear stress in vascular grafts.

Tube feet dynamics drive adaptation in sea star locomotion

This study shows sea stars adjust tube foot adhesion time based on body load and orientation to adapt locomotion without a central nervous system.

Integrated Cross-Species Translation and Biophysical Multi-Scale Modeling Links Molecular Signatures and Locomotory Phenotypes in Spaceflight-Induced Sarcopenia

The paper identifies conserved molecular pathways in spaceflight-induced sarcopenia using cross-species analysis and develops a model linking transcriptional changes to locomotion deficits.

Cost-effective early detection of banana bunchy top disease: insights from spatio-temporal modelling in Benin

The paper uses spatio-temporal modeling to evaluate cost-effective strategies for early detection of banana bunchy top disease in Benin, finding that early detection is expensive but feasible with optimized sampling.

Spontaneous Phase Separation Enables Rapid, Polymerization-Free Fabrication of Dissolvable Hydrogels

This paper demonstrates a polymerization-free hydrogel fabrication method using spontaneous phase separation, enabling encapsulation of live cells, antibiotics, and plant seeds.

The C terminus of infectious bursal disease virus (IBDV) VP3 encodes a predicted intrinsically disordered region (IDR), which promotes the formation of cytoplasmic puncta and modulates their physical properties.

Highly under-actuated dynamic manipulation: Dice stacking is mostly open-loop

The paper shows that dice stacking, a dynamic manipulation task, can be performed open-loop without state feedback, using simulations and a physical robot.

Critical Scaling of Novelty in the Cortex

The paper shows novel spikes in the cortex disproportionately influence neighboring neurons through power-law scaling, suggesting critical dynamics enable efficient novelty detection.

Mitochondrial control of fuel switching via carnitine biosynthesis

SLC25A45 is the inner mitochondrial membrane transporter for trimethyllysine required for de novo carnitine biosynthesis, enabling metabolic fuel switching to fatty acid oxidation during cold exposure and semaglutide treatment.

Role of Water Models in Simulations of Ion Conduction in Potassium Channels

The paper uses molecular dynamics simulations to show that both hard and soft knock-on mechanisms of ion conduction in potassium channels are accessible and reversible, depending on simulation parameters.

From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture

The paper introduces 4DGBWorkflow and 4DGB, open-source tools that use molecular dynamics simulations constrained by Hi-C data to generate 3D chromatin reconstructions and integrate them with epigenomic data for visualization.

Ultrasound Transparent Neural Interfaces for Multimodal Interaction

This paper develops ultrasound-transparent neural interfaces that enable compatibility with functional ultrasound imaging and therapy, validated through simulations and experiments.

Atypical collective oscillatory activity in cardiac tissue uncovered by optogenetics

The paper investigates how external stimuli induce ectopic arrhythmias in cardiac tissue with localized depolarization, revealing bi-stable oscillatory behavior controlled by stimulus frequency.

DNA Actively Regulates the "Safety-Belt" Dynamics of Condensin during Loop Extrusion

This study reveals how DNA actively regulates condensin's safety-belt dynamics through multiscale simulations, showing DNA's role in stabilizing and modulating loop extrusion.

Systems-level Consequences of Low RAF Abundance for EGFR-ERK Signaling

The paper develops computational models of the EGFR-ERK pathway to show that low RAF abundance creates signaling bottlenecks and stochastic dynamics, affecting ERK activation and RAS-RAF interactions in cancer cells.

The use of cross-validation has overestimated the value of genomic selection in plant breeding

The paper argues that cross-validation overestimates genomic selection's effectiveness in plant breeding, especially when used for accuracy improvement rather than selection intensity.

Delta PSA: A New Metric for Conformational Dynamics Underlying Macrocyclic Peptide Permeability

The paper introduces Delta PSA, a metric for predicting macrocyclic peptide permeability using MD simulations, achieving lower MSE than existing methods.

Real-Time GPU-Accelerated Digital Heart Twin: Integrating Bidirectional Interactions Between Living Optogenetic Monolayers and Computational Simulations

This paper develops a real-time digital heart twin system that integrates optogenetic cardiac monolayers with GPU-accelerated simulations to study reentrant arrhythmias.

The membrane transition strongly enhances biopolymer condensation through prewetting

The paper shows that membrane prewetting enhances biopolymer condensation by lipid composition, observed in simulations, reconstitution, and cells.

Reducing type II error in fMRI analysis: Cluster-extent threshold simulation results and an evaluation of current methods to correct for multiple comparisons

This study shows that incorporating sample size into fMRI cluster threshold calculations reduces type II error and improves accuracy.

1100 Synthetic Benchmark Problems for Dynamic Modeling of Cellular Processes

The paper introduces 1100 synthetic benchmark problems for dynamic cellular process modeling to improve algorithm evaluation.