simulation

Firing rate adaptation in grid cells produces macroscopic hexadirectional modulation

The paper investigates the neuronal origin of hexadirectional modulation in grid cells using data from foraging rats, finding that firing rate adaptation explains the phenomenon.

Examining the Atypical Structure Adopted by the 37-51 Segment of α-synuclein in the Early Stage of Aggregation

This study uses molecular dynamics simulations to identify a previously unreported braid conformation in the 37-51 segment of α-synuclein that may influence aggregation.

Direct engagement of mycobacterial RadA by c-di-AMP at a non-catalytic site suppresses its DNA-stimulated ATPase activity

This study shows c-di-AMP binds to Mycobacterium smegmatis RadA at a non-catalytic site, reducing its DNA-stimulated ATPase activity.

Bats Could Learn Three-Dimensional Echolocation Using Echoacoustic Flow

This paper shows a simulated bat-like agent can learn its echolocation-related transfer function (ERTF) using echoacoustic flow without external guidance or labeled data.

Computational assay of hERG ion permeation and its modulation by small-molecule compounds

This study uses molecular dynamics simulations to investigate hERG ion permeation and how small molecules modulate it, revealing structural mechanisms and binding modes.

Computational Profiling and Pathogenicity Assessment of VHL Missense Mutations

This study assesses the pathogenicity of VHL missense mutations using AlphaMissense, protein stability simulations, and molecular dynamics to identify critical regions and mutation effects.

The Joint Impact of Deleterious Mutations, Dominance, and Gene Flow on Linked Neutral Variation in Structured Populations

The paper investigates how deleterious mutations, dominance, and gene flow affect neutral genetic variation in structured populations using simulations and genealogical analyses.

An Efficient Implicit Tau-Leaping Method for Estimating Second-Order Sensitivities of Stiff Stochastic Biochemical Systems

The paper introduces an efficient implicit tau-leaping method to estimate second-order sensitivities of stiff stochastic biochemical systems, achieving comparable accuracy with reduced computational cost.

Optimizing Cognitive Phenotyping for Genetic Discovery in Alzheimer's Disease: A Simulation-Based Evaluation of Mini-Mental State Examination-Based Decline Measures

The paper evaluates cognitive decline measures for genetic studies in Alzheimer's disease using simulations, finding that simpler measures like Slope and dMMSE/dt are more powerful.

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

From Coral Color to Tissue Heating: How Host Pigments Redirect Light Within the Tissue

The paper models how coral host pigments affect light propagation and tissue heating, showing distinct roles of chromoproteins and fluorescent proteins in energy distribution and heat generation.

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

The impact of strain heterogeneity on genomic profiling accuracy in mixed-strain Escherichia coli metagenomes

The paper evaluates how strain heterogeneity affects the accuracy of genomic profiling in mixed-strain Escherichia coli metagenomes using simulated data and various bioinformatic tools.

Integrating Genetic Domestication and Model-Guided Kill-Switch Engineering in a Non-Model Bacterial Therapeutic

Host-measured parts and inducible systems for Brucella melitensis ΔvjbR guided a modeled Cas9 kill-switch, which cut mouse liver bacterial burden by about 91% at 30 mg/kg doxycycline.

Mechanistic Insights into Adaptive Binding of Vitamins and Hormones at Hotspot-Enriched Interfaces of the Synaptotagmin 1 C2AB Domain

This study investigates the adaptive binding of seven molecules to the Synaptotagmin 1 C2AB domain using molecular docking and simulations, revealing that desolvation and structural flexibility, not just binding energy, govern ligand interactions.

Synaptotagmin-mediated plasma membrane homeostasis is required to recruit the endocytic machinery during cold stress

This study shows that SYT1 and SYT3 are essential for maintaining endocytosis during cold stress in Arabidopsis by preserving membrane composition and TPC subunit association.

Optimal MR-ARFI encoding parameters for a range of contemporary magnetic field gradient systems

The paper optimizes MR-ARFI gradient parameters and provides a simulation tool to enhance sensitivity under various hardware conditions.

Strain resolution and wide relative abundance quantification of bacterial microbiomes with nanopore sequencing of the ribosomal RNA operon

This paper demonstrates strain-level resolution and quantification of bacterial microbiomes using nanopore sequencing of the ribosomal RNA operon, showing accurate relative abundance quantification over multiple orders of magnitude.

Hemodynamic-Structural Multi-Fidelity Assessment of Endovascular Flow Diversion Strategies for Cerebral Aneurysm Treatment: An Integrated Computational and Experimental Framework

The paper evaluates hemodynamic and structural outcomes of endovascular flow diversion strategies for cerebral aneurysms using computational models and experimental tests.

Protein Crowding Buffers Membrane Fluidity

This study shows that protein crowding reduces lipid order in membranes, eliminating the liquid-gel phase transition similar to cholesterol's effect.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

To mix or to de-mix?: Cation-π suppresses heterogeneity in local structure and dynamics of heterotypic Condensates

This study shows cation-π interactions reduce heterogeneity in heterotypic condensates by enhancing stability and mixing.

VASP association stabilizes the actin nucleus revealed by molecular dynamics simulations

This study uses molecular dynamics simulations to show that VASP stabilizes actin trimers by preferentially anchoring a subunit and preserving conformational heterogeneity.

Channelrhodopsin Ion Selectivity Determines Mechanisms and Efficacy of Optogenetic Defibrillation in Human Atria and Ventricles

This study compares the defibrillation efficacy of different channelrhodopsins in human cardiac tissue using simulations, finding that ion selectivity affects arrhythmia termination mechanisms and success.

Hybrid Drosophila genomes rapidly purge minority ancestry but repeatedly retain selected regions

The paper tracks genome-wide evolutionary dynamics in hybrid Drosophila populations, showing rapid purging of minority ancestry and repeated retention of selected regions through adaptive introgression.

In Silico Design and Comprehensive Evaluation of a Novel Multi-Epitope Vaccine Candidate Against Chandipura Virus

This paper designs and evaluates a multi-epitope vaccine candidate against Chandipura virus using computational methods, showing strong antigenicity, low allergenicity, and predicted immune response.

A Sense of Direction: Detecting Natural Selection Across Non-Stationary Genomes

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination

The paper presents DeFluorX, a pipeline using Boltz-2 to identify FAcD variants for PFAS defluorination by analyzing geometric and energetic factors in enzyme-PFAS complexes.

Decoding CBM2 binding modes: how similar folds achieve distinct substrate preferences

This study investigates how CBM2 proteins achieve distinct substrate preferences through a balance of topological complementarity, hydrophobic dehydration, and hydrogen-bonding interactions.