simulation

Early Steps in Pathogen-induced TTR-amyloid-formation

The paper uses molecular dynamics simulations to investigate if SARS-CoV-2 peptides can initiate TTR tetramer dissociation, leading to amyloidosis.

Division of labor during bacterial warfare

The paper investigates bacterial warfare by analyzing toxin production in Escherichia coli, finding that localized toxin bursts are more effective than uniform production in structured populations.

Comparing Livestock Mobility-Informed Strategies for Peste des Petits Ruminants Control in Nigeria: The Central Role of the Network Backbone

The paper compares PPR control strategies in Nigeria using a livestock mobility network, finding that targeting the network backbone is most effective in reducing epidemic outcomes.

Seven amino acids gate transcriptional activation by a minimal MarA Helix turn-helix DNA-binding domain

The paper shows that a single HTH domain from MarA can bind DNA and activate transcription when properly dimerized, revealing structural insights for synthetic biology applications.

Recombination accelerates adaptation across genetic architectures and demographic histories

This study shows that higher recombination rates modestly speed up adaptation in populations, primarily by reducing Hill-Robertson interference, with effects varying by demographic history.

The nanoscopic submyelin space mediates efficient K+ uptake and shapes nodal action potentials

The paper develops a finite element model to study K+ dynamics and action potential behavior at the node of Ranvier, revealing how periaxonal K+ buffering enables high-frequency conduction.

An Excelled Trifluorinated Probe for GPCR Conformational Quantification

This paper introduces a novel 19F-labeled probe, BTMB, for studying GPCR conformational dynamics and demonstrates its advantages over existing probes through molecular dynamics simulations.

Eco-evolutionary dynamics create extinction avalanches in mutualistic-antagonistic networks

This study shows how evolution can trigger abrupt extinction events in ecological networks through self-organized dynamics, highlighting the role of interaction types in biodiversity loss.

Navigating between global robustness and fine-scale resolution: the potential of demographic inference based on identical-by-descent segments.

This study evaluates two IBD-based methods for estimating effective density and dispersal variance, finding that IBD-Analysis performs better under spatially homogeneous conditions while MAPS captures spatial patterns but introduces noise in uniform landscapes.

Signal peptidase complexes set species-specific rules for signal peptide cleavage

The paper shows that human signal peptides are inefficiently cleaved by yeast SPCs due to differences in SPC-lipid interactions and membrane thinning profiles.

Host-dependent salivary effector candidates and predicted plant immune targets in Spodoptera frugiperda

The paper identifies host-dependent salivary effector candidates and predicted plant immune targets in Spodoptera frugiperda by analyzing transcriptomes and predicting protein interactions.

Designing spatial capture recapture surveys for multiple populations

This paper evaluates SCR survey designs for multiple populations, showing systematic layouts perform well despite group differences.

Constructing Virtual Viruses in A Spatial Minimal Cell

The paper constructs virtual viruses within a spatial minimal cell to model viral development and host interactions.

On the neural origin of hexadirectional fMRI modulations

The paper proposes experiments to distinguish mechanisms underlying hexadirectional fMRI modulations linked to grid-cell activity.

Microswitch-Guided Sampling for the Detection of Ligand Signaling Bias in GPCR Systems

This paper introduces MGS, a computational method to detect ligand signaling bias in GPCR systems by analyzing conformational changes linked to specific signaling pathways.

Computational simulation reveals the critical role of spike-timing-dependent plasticity in synchrony

The paper uses computational simulations to show that spike-timing-dependent plasticity (STDP) regulates synchronization and desynchronization dynamics, resolving the synchronization/desynchronization conundrum.

The quasi systematic nature of splitter cells

This study shows splitter cells are not necessary for task performance, as their removal allows network reorganization to maintain behavior.

Breaking Pore Symmetry to Prolong DNA Residence in Solid-State Nanopores

This paper demonstrates that tilting solid-state nanopores increases DNA dwell time by altering electric field distribution and DNA motion, enhancing single-molecule sensing capabilities.

Removal of Hg and Cu from raw gold-mine tailings by microalgae- and bacteria-augmented microbial fuel cells: Effects of bio-augmentation, diurnal cycling and operational faults

This study evaluates the effectiveness of microbial fuel cells in removing mercury and copper from gold-mine tailings, finding that physicochemical processes, not algal bio-augmentation, drive contaminant removal.

Computational modeling of an RNA-peptide world

This study uses computational simulations to show that short random peptides enhance RNA evolution and structural diversity, suggesting an RNA-peptide world in early life.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Dynamic Pocketome of Trace Amine-Associated Receptors

The paper presents a dynamic pocketome analysis of TAAR receptors using simulations, revealing receptor-specific ligand-receptor interplay and plasticity in binding sites.

Computing the geometry of phase-amplitude coupling: A new moment-based framework

This paper introduces a moment-based framework to analyze phase-amplitude coupling geometry, revealing that traditional metrics can obscure geometric differences.

Dual Carbohydrate Recognition by the Chitinase-like Protein CHI3L1 Through Distinct Glycosaminoglycan and Chitin-Binding Interfaces

This study identifies two distinct carbohydrate-binding sites on CHI3L1, showing that chitin oligosaccharides and glycosaminoglycans bind to separate sites with different affinities and regulatory effects.

Learning to play with spikes: characterizing, predicting, and engineering unsupervised plasticity rules for spiking reservoir computing

This paper characterizes and predicts effective unsupervised plasticity rules for spiking reservoir computing by analyzing their performance on a Pong game task.

Active control of surface immobilization in the foraging behavior of Paramecium

Paramecium tetraurelia alternates fast swimming with minutes-long surface immobilization when bacteria are present; stops require calcium influx and come from halting locomotor cilia while oral cilia keep beating.

MAT-classifier: A memory-efficient pipeline for accurate genus level profiling from ancient metagenomic data

Per-genus Bowtie2 or BWA-aln alignments in place of MALT cut alignment-stage memory from about 140 GB (aMeta) to about 7 GB and gave higher simulated-data AUC (0.87 vs 0.79).

Simulated field potentials capture multiple simultaneous processes underlying human temporal attention

The paper simulates field potentials to disentangle neural mechanisms of human temporal attention, identifying signatures of attentional bias and anticipatory activity that predict perceptual accuracy.

Analysis of the off-target interaction of amyloid PET tracers with human brain sulfotransferases

The paper investigates off-target interactions of amyloid PET tracers with brain sulfotransferases using multi-omic and computational methods, revealing enzyme-specific binding dynamics and implications for PET signal variability.

Incomplete references leave bulk deconvolution targets non-identifiable, but identification has a computable precision price

With an incomplete deconvolution reference, operator history changes estimates and associations, and the target is not point-identified; fitdrop scores remedies on shrinkage, coverage, certification and false certification, and prices measurements.