simulation

Multi-Target In Silico Investigation of Withaferin A as a Potential Antiviral Inhibitor Against Key Marburg Virus Proteins

This study evaluates Withaferin A's antiviral potential against Marburg virus proteins using computational methods, showing favorable binding and ADMET properties.

Characterizing the Conformational Dynamics of an Intrinsically Disordered Localization Sequence

This study examines how single-residue substitutions in a mitochondrial localization peptide affect its conformational dynamics, revealing that sequence changes can bias structural ensembles and influence targeting efficiency.

Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome

The paper identifies two previously unknown oral bacteria in infants and shows they co-occur and exchange nutrients through metabolic interactions.

Cascades and convergence: dynamic signal flow in a synapse-level brain network

The paper simulates sensory signal propagation in the Drosophila connectome to study modality-specific cascades and neuron classification based on dynamic response profiles.

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

Vegetated urban spaces increase Aedes albopictus survival and the risk of Dengue and Chikungunya Transmission: a field and modelling study in Montpellier, France

This study finds that vegetated urban areas increase Aedes albopictus survival and arboviral transmission risk by analyzing field data and modeling R0 for Dengue and Chikungunya in Montpellier.

NMDAR-mediated shift of neuronal gain across the cortical hierarchy

This study shows that NMDA receptors adjust neuronal gain across the cortical hierarchy, allowing integration of dense presynaptic inputs.

A simulation-based deep learning framework for spatially explicit malaria modeling of CRISPR suppression gene drive mosquitoes

This study uses a simulation-based deep learning model to analyze how different parameters affect mosquito suppression and malaria prevalence in Anopheles gambiae.

Sex-biased dispersal drives mito-nuclear discordance in simulated populations

This study uses simulations to show that sex-biased dispersal amplifies mito-nuclear discordance, which arises from differences in effective population sizes.

Absorption dipole effects on MINFLUX single molecule localization

This paper investigates how absorption dipole orientation affects MINFLUX localization accuracy, finding that tilted dipoles introduce biases that depend on their orientation and position within the imaging area.

Fundamental limits on patterning by Turing-like reaction-diffusion mechanisms

This paper investigates complex reaction-diffusion models to understand patterning constraints and introduces a software pipeline for simulating these systems.

Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins

The paper investigates how sequence variation affects the dynamics of intrinsically disordered proteins, finding that reconfiguration times are largely independent of sequence despite changes in chain dimensions.

Antagonist binding actively disrupts interleukin-1 receptor dynamics to block co-receptor recruitment

This study shows antagonist binding disrupts IL1R1 dynamics to block co-receptor recruitment, contrasting with agonist-induced stabilization of signaling conformations.

Simulations reveal hybridization in Caribbean Acropora restoration poses low risk of genetic swamping but limited potential for adaptive introgression

The paper uses simulations to assess risks and benefits of hybridization in Caribbean coral restoration, finding low genetic swamping risk and limited adaptive introgression potential.

Simulation and empirical evaluation of biologically-informed neural network performance

The paper evaluates how dataset characteristics affect biologically-informed neural network performance using simulations and empirical testing with prostate cancer data.

Large-scale simulations reveal evolutionary constraints on intrinsically disordered regions imposed by full-length protein architecture

The paper uses large-scale simulations to show that intrinsically disordered regions in proteins are structurally and evolutionarily constrained by their full-length protein architecture.

Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets

The paper benchmarks tools for locus-specific TE analysis in scRNA-seq, finding older TEs are more accurately quantified, while young TEs face challenges due to multi-mapping reads.

The refresh rate of overhead projectors may affectthe perception of fast moving objects: a modellingstudy

This study models how overhead projector refresh rates may influence the perception of fast-moving objects at retinal, cortical, and psychophysical levels.

Transcriptome-based lead generation, ligand- and structure-based prioritization and experimental validation of TLR5-activating molecules

This paper generates TLR5-activating molecules using a systems-level approach combining transcriptome data and computational methods, validated experimentally.

Imbalance in gut microbial interactions as a marker of health and disease

A gut consumer-resource model with explicit metabolic pathways yields competition-dominated healthy and cooperation-dominated dysbiotic states; an interaction-balance index (ENBI) detects this shift in human disease cohorts.

Residual ellipticity in waveplate-compensated polarization-resolved SHG microscopy may arise from femtosecond laser spectral bandwidth

This study investigates residual polarization ellipticity in waveplate-compensated polarization-resolved SHG microscopy and identifies femtosecond laser spectral bandwidth as a potential cause.

Condensate-Driven Transcriptional Reprogramming Defines Core Vulnerabilities in Esophageal and Gastric Cancers

The paper identifies condensate-driven transcriptional programs in esophageal and gastric cancers, showing their role in tumor viability and suggesting therapeutic targets.

Oncogenic chromodomain mutations allosterically impair TIP60 acetyltransfearse function preventing activation of DNA repair genes under genotoxic stress

This study identifies how chromodomain mutations in TIP60 impair its acetyltransferase function, leading to reduced DNA repair gene activation and genomic instability.

Targeting immunometabolic pathways with AZD1656 alleviates inflammation and metabolic dysfunction in type 2 diabetic cardiomyopathy

In db/db mice, six weeks of AZD1656 improved diastolic function, cardiac metabolism and infarct size, with increased Treg infiltration and less fibrosis, without glycaemic change.

Tracing Neanderthal ancestry patterns through successive population expansions in Europe

This study uses a simulation framework to analyze how Neanderthal ancestry gradients in Europe were shaped by population expansions and interactions between Neanderthals, hunter-gatherers, and farmers.

Geoclimatic oscillations and ancient reciprocal adaptive introgression shape the evolutionary trajectories of threatened Coilia

This study reconstructs the evolutionary history of Coilia species, revealing ancient reciprocal introgression and its role in adaptation to geoclimatic changes.

Flow constraints at infection site shape multiplication-dissemination trade-offs and opposite regulatory programs of Xanthomonas and Ralstonia xylem pathogens

This study shows how xylem sap flow constraints shape opposite regulatory strategies in two plant pathogens, Xcc and Rs, to mitigate trade-offs between virulence traits.

Recombination and the role of pseudo-overdominance in polyploid evolution

The paper simulates evolution in diploid and autotetraploid populations to show that pseudo-overdominance is more common in polyploids due to reduced recombination and increased masking of deleterious mutations.

Intercellular forces driving stratification in a two-layer corneal epithelium: Insight from a Voronoi cell-based simulation model

This paper develops a Voronoi cell-based simulation model to study corneal epithelial stratification, revealing how cell delamination and mechanical forces drive tissue renewal and repair.

Back to the future 2: the implications of germplasm structure on thebalance between short and long-term genetic gain in a changingtarget population of environments

The paper investigates how environmental changes affect genetic gain in plant breeding by simulating germplasm structure and selection strategies.