simulation

Membrane Thickness Strain from Protein Inclusions: A Multiscale Simulation and X-Ray Scattering Study of Proteoliposomes

This study uses multiscale simulations and X-ray scattering to quantify membrane strain caused by protein inclusions in proteoliposomes, showing agreement between simulations and experiments.

Evolutionary dynamics of temporal transcription factor series in the insect visual brain

This study reconstructs the evolutionary history of temporal transcription factor series in insect visual brains, showing conserved patterns and species-specific variations that influence neuronal diversity.

Growth and patterning in vertebrate limb developmentA timescale perspective on skeletal specification

This paper introduces a computational framework to model limb skeletal patterning in mice and axolotls by integrating growth, gene regulation, and signaling spread, showing varying contributions of these factors across limb regions.

A Multidimensional Analysis of the Bimodal Piperaquine Response in Plasmodium falciparum

The paper investigates the bimodal piperaquine response in Plasmodium falciparum by analyzing metabolic, transcriptional, and molecular dynamics data to identify the role of plasmepsin II/III copy number and pfcrt mutations.

Simulation of neurotransmitter release and its imaging by fluorescent sensors

The paper presents a kinetic Monte Carlo framework to simulate neurotransmitter release and fluorescent sensor imaging, showing how sensor location and kinetics affect fluorescence images.

Coordinated subpocket engagement underlies nitazene potency at the μ-opioid receptor.

The paper identifies structural determinants of nitazene potency at the μ-opioid receptor using functional assays, quantum mechanics, and molecular dynamics simulations.

Simulating population pangenomes under coalescent demographic models with MSpangenome

MSpangenome simulates population pangenomes from coalescent demographic models to benchmark graph construction tools.

Dancing to the beats of the mammalian connectome: Topological and dynamical asymmetries shape infra-slow oscillations

The paper shows that topological and dynamical asymmetries in brain networks generate infra-slow oscillations through coupled oscillator models.

Drug Functional Site-Unknown Molecular Targets Exemplified by SARS-CoV-2 pseudoknot and ribosomal frameshifting-modulators

This paper identifies FDA-approved drugs that modulate SARS-CoV-2 -1 PRF by altering RNA pseudoknot folding dynamics, demonstrating a strategy for targeting structured RNAs.

Near-critical slow dynamics enable flexible temporal computations and generalization

This paper investigates the role of slow dynamics in neural computation, showing that structured transient dynamics enable temporal computation and generalization.

Calcium Dependent Conformational Changes in Human Transglutaminase 2 and its Implications in Celiac Disease

This study investigates calcium-dependent conformational changes in TG2 and their role in celiac disease using molecular dynamics and nsSNP analysis.

Collective fluctuations underlying nanobody inhibitory activity targeting B. anthracis S-layers revealed by multiscale simulations

This study uses multiscale simulations and machine learning to show that nanobodies induce local fluctuations in B. anthracis S-layer proteins, leading to lattice-scale disassembly and pathogenicity inhibition.

Evaluating camera trap methods for monitoring population trends in ungulates: insights from simulation

This study evaluates camera trap methods for detecting population trends in ungulates using simulations, finding that both REM and IS methods struggle to detect population declines despite ideal conditions.

The effects of post-divergence gene flow on simultaneous divergence time (SDT) testing

This study evaluates how post-divergence gene flow affects the accuracy of simultaneous divergence time estimates using simulations and Bayesian methods.

Spatially explicit capture-recapture models for relative density

Maximizing the conditional likelihood in spatially explicit capture-recapture models estimates spatial relative density and population growth rates rapidly while remaining robust to unmodeled individual detection heterogeneity.

Mutation-Induced Pocket Deactivation: How Ser353/Pro245 Alters KCa2.2 vs KCa3.1 Ligand Selectivity

This study identifies Ser353/Pro245 as the key structural determinant for ligand selectivity differences between KCa2.2 and KCa3.1 channels using computational methods.

Spatial Recruitment Model for Motor Potentials Evoked By Transcranial Magnetic Stimulation (TMS) for In-Silico Testing and Tuning of Closed-Loop Procedures

The paper develops a population model of motor evoked potentials from TMS to enable in-silico testing and tuning of closed-loop procedures without experimental data.

Modelling individual ampullary afferents in two species of gymnotiform fish using simulation-based inference

The paper develops a mechanistic model of ampullary electroreception in two electric fish species using simulation-based inference to capture response properties and spectral characteristics.

Complete Enzyme Clustering Enhances Coenzyme Q Biosynthesisvia Substrate Channeling

The paper investigates how metabolon clustering enhances coenzyme Q biosynthesis through substrate channeling using simulations and experiments.

Computational Insights into the tACS Modulation in Healthy and Epileptic Brain Networks

This study uses a neuroinspired model to investigate how tACS and tDCS affect neural activity in healthy and epileptic brain states, showing frequency entrainment in healthy networks and reduced hyperexcitability in epileptic networks.

Critical Scaling Laws and Universality Classes in Biomolecular Condensates

The paper investigates criticality in biomolecular condensates using simulations, identifying critical exponents and two universality classes based on molecular interactions.

LOESS and DE-SWAN can induce artifactual "waves" of molecular aging

This paper shows that LOESS and DE-SWAN can create false 'waves' of molecular aging in data, challenging previous conclusions about discrete aging patterns.

A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels

The paper develops and validates Sparse-Seq, a low-coverage sequencing method for accurate quantification of 5mC and 5hmC levels, showing it is more accessible and less variable than mass spectrometry.

Intrinsic molecular susceptibility underlies selective neuronal vulnerability in the Alzheimer's disease entorhinal cortex

The paper identifies intrinsic molecular features of calbindin-expressing neurons in the entorhinal cortex that contribute to their vulnerability in Alzheimer's disease and suggests potential therapeutic targets.

Extinction risk in terrestrial vertebrates is associated with niche limits that reflect climatic vulnerability

The paper links extinction risk in terrestrial vertebrates to climatic niche limits, showing that species with colder thermal tolerances are more threatened and that future extinctions will disproportionately impact climatically vulnerable lineages.

Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles

This study uses in-silico DBTL cycles to evaluate how process parameters affect strain optimization outcomes in metabolic engineering.

PP-MAPS: dynamic pharmacophore signatures of protein-peptide interfaces from molecular dynamics trajectories

PP-MAPS extracts dynamic pharmacophore signatures from MD trajectories of protein-peptide complexes to analyze interactions and compare peptides and binding sites.

Neuromorphic hierarchical modular reservoirs

This paper introduces hierarchical modular networks as reservoirs to study computational advantages of brain-like modularity, showing enhanced memory, multitasking, and temporal dynamics.

ATAClone: Cancer Clone Identification and Copy Number Estimation from Single-cell ATAC-seq

ATAClone identifies cancer clones and estimates copy numbers from scATAC-seq data, improving accuracy over existing methods.

fastQpick: scalable bootstrap and subsampling of FASTQ reads

fastQpick generates bootstrap replicates of FASTQ reads for uncertainty quantification in sequencing data.