simulation

Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness

This study uses simulations to show how varying stiffness in polymers affects their collapse and adsorption in crowded environments, with flexible regions promoting collapse and semiflexible regions influencing adsorption.

In silico characterization of unique fungal modular rhodopsin expands the horizon of novel optobiological and biomedical applications

The paper identifies novel fungal modular rhodopsins through in-silico analysis and suggests their potential roles in light-driven signaling and biosynthetic regulation.

Multi-Scale Simulations of Excited-State Energy Transfer Pathways in the C2S2-Type PSII-LHCII Supercomplex of Spinach

The paper uses simulations to show how energy transfer in PSII-LHCII supercomplexes is directional despite a flat energy landscape, identifying key pathways and dynamic regulation mechanisms.

A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection

This study evaluates long single-end barcoded reads for structural variant detection, showing improved accuracy with longer read lengths compared to short-read and pangenome-based methods.

Modeling tumor transport and growth with poroelastic biopolymer networks

This study models how poroelastic properties of the extracellular matrix affect tumor growth and transport through hydrogel experiments and computational simulations.

Multi-modal Monte Carlo MRI simulator of tissue microstructure

The paper introduces a multi-modal Monte Carlo MRI simulator that models tissue microstructure's impact on various MRI sequences and validates it against established techniques.

GeneSNAKE: a Python package for benchmarking and simulation of gene regulatory networks and perturbation-induced expression data

GeneSNAKE is a Python package that simulates gene regulatory networks and perturbation-induced expression data for benchmarking, offering control over network properties and noise models.

How human-derived brain organoids are built differently from brain organoids derived of genetically-close relatives: A multi-scale hypothesis

The paper proposes a multiscale hypothesis to explain structural differences in brain organoids derived from human versus genetically close non-human primate stem cells, linking chromatin reorganization to delayed cell fate transitions.

Structural Determinants for the Monomeric and Phospholipid-Transport P4B-ATPase via comprehensive in silico analysis of P4-ATPase structures.

This study identifies structural determinants of P4B-ATPases through in silico analysis, revealing unique features that may underlie their monomeric phospholipid transport mechanism.

Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis

This study shows chronic infections can generate SARS-CoV-2-like mutation bursts without epistasis, increasing global evolutionary rates.

Linking local and large-scale salient events with oscillatory and broadband arrhythmic activities in the resting human brain

This paper introduces a framework linking oscillatory and broadband activities to transient salient events in resting brain data, showing how they emerge from spectral properties and interactions.

NeighborFinder: an R package inferring local microbial network around a species of interest

R package NeighborFinder infers a focal species' co-abundance neighbors via repeated cross-validated ℓ1 regression, reaching F1 ≥ 0.95 on simulated cohorts of 250 to 1000 samples.

MagPiezo: a Magnetogenetic Platform for Remote Activation of Endogenous Piezo1 Channels in Endothelial Cells

MagPiezo pairs 19 nm anti-Piezo1-conjugated ZnMnFe2O4 nanoparticles with a 1 Hz, <40 mT magnetic applicator to generate piconewton torque that gates endogenous Piezo1 channels in human endothelial cells.

Excessive Censoring Degrades Individual-Specific Cortical Parcellations and Personalized TMS Targets

The paper evaluates how different censoring strategies affect cortical parcellations and TMS targets in rs-fMRI, finding that lenient censoring yields better results than strict censoring.

Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

The paper compares methods for analyzing heterogeneity in TRPV1 cryo-EM data and finds that different methods detect different types of heterogeneity.

Benchmarking Free Energy Computational Methods for Revealing the Interactions Driving PARP1 Selective Inhibition

This study benchmarks computational methods to predict PARP1 vs PARP2 inhibitor selectivity, finding FEP and PMF outperform MM/PBSA in accuracy.

Bimodal mechanical response of membrane necks: Implications for the nuclear envelope.

This study investigates how membrane neck size responds to pressure gradients, revealing a two-phase behavior with implications for nuclear envelope mechanics and synthetic membrane design.

Ligand-Induced Structural Dynamics Drive Allosteric Regulation of Translation Initiation Factor eIF4E

This study investigates how two structurally similar ligands, 4EGI-1 and i4EG-BiP, regulate eIF4E through distinct binding modes, revealing that frontal binding promotes 4E-BP1 over eIF4G interaction.

Dopaminergic Control of Retinal Oscillations Driving Infantile Nystagmus

This paper identifies dopaminergic modulation of AII amacrine cells as a therapeutic target for infantile nystagmus by showing that restoring dopamine suppresses retinal oscillations and improves visual signal fidelity.

A Model to Simulate the Interference Effects of Acute Aerobic Exercise on Rate of Force Development in Weightlifters

This paper builds a model to simulate how acute aerobic exercise affects rate of force development in weightlifters and develops a prediction equation for interference effects.

Mechanism of Tethered Agonist Binding to an Adhesion G-Protein-Coupled Receptor

This study uses Pep-GaMD simulations to reveal how a tethered agonist transitions from a β-strand to a U-shaped helical configuration upon binding to ADGRD1.

Resource ratio fluctuations drive the evolution of microbial metabolic strategies

The paper shows that resource ratio fluctuations drive the evolution of microbial metabolic strategies, with balanced environments favoring specialists and imbalanced ones favoring generalists.

LIVN: A testbed for learning to interact with in vitro neural networks

The paper introduces LIVN, an open-source simulation environment for developing and testing machine learning models to control in vitro neural networks using synthetic data with ground truth.

Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses

The paper investigates MALT1 activation dynamics using a combination of AlphaFold, MD simulations, and NMR analyses, revealing how ionic strength influences its conformational states.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

A simple network of proprioceptive reflexes can produce a variety of bipedal gaits

This paper demonstrates that a simple reflex-based control system can generate diverse bipedal gaits without rhythmic inputs or high-level state machines.

Whole-brain connectomics of Drosophila reveals a robust, distributed architecture for the suppression of feeding during escape

The paper simulates Drosophila's connectome to show how escape behavior suppresses feeding through a distributed, redundant neural architecture.

Determining the driving factors shaping genetic architecture of complex traits in recently admixed populations

This study evaluates how admixture, selection, and demographic history influence GWAS power and fine-mapping precision in admixed populations using simulations and empirical data.

Universal genomic constraints in the evolvability of thermal physiology

The paper uses simulations to show that body temperature evolution is constrained by protein thermal performance, leading to predictable patterns of rapid initial change followed by slow adaptation.

A Biologically Grounded Structural Causal Model Enables cfRNA Specific In-Context Learning

The paper introduces cfRNA-ICL, a model trained on synthetic data generated from a biologically grounded SCM, showing improved performance in cancer classification tasks compared to generic models.