simulation

Impact of the Microtubule Cytoskeleton on Insulin Transport in Beta Cells: A 3D Computational Study

This paper develops a 3D computational model to study how the dense microtubule network in beta cells affects insulin vesicle mobility and secretion, finding that caging by microtubules impairs vesicle movement and reduces insulin availability.

ReaxFF-guided Optimisation of VIRIP-based HIV-1 Entry Inhibitors

This paper optimizes a HIV-1 entry inhibitor peptide using ReaxFF molecular dynamics simulations, reducing its size while maintaining or improving antiviral activity.

Temporal dose inversion properties of adaptive biomolecular circuits

The paper demonstrates temporal dose inversion in adaptive biomolecular circuits using synthetic gene circuits and identifies key parameters for this behavior.

Cryo-EM ligand building using generative AI and molecular dynamics

This paper develops a method combining generative AI and molecular dynamics to improve ligand modeling in cryo-EM maps of protein-ligand complexes.

Computation-through-DynamicsToolkit: Simulated datasets and quality metrics for dynamical models of neural activity

The paper introduces CtDToolkit, a framework providing synthetic datasets and metrics to evaluate and improve neural dynamics models of neural computation.

Modeling cryo-EM structures in alternative states with generative AI and density-guided simulations

The paper improves modeling of cryo-EM maps for membrane proteins with multiple states using generative AI and density-guided simulations.

The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

The paper evaluates demultiplexing methods for joint snRNA/snATAC experiments under ambient contamination and introduces a new metric to assess their performance.

Massive Compression for High Data Rate Macromolecular Crystallography (HDRMX): Impact on Diffraction Data and Subsequent Structural Analysis

The paper evaluates lossy compression methods for high data rate macromolecular crystallography to minimize information loss while maintaining structural analysis quality.

Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors

This study uses PPI-GaMD simulations to reveal dynamic mechanisms of peptide agonist dissociation and deactivation in ADGRG1 and ADGRG2.

Modelling and simulation of the interactions between the cardiovascular system, VA ECMO and IABP: when is it an appropriate combination?

The paper simulates interactions between cardiovascular system, VA ECMO, and IABP to evaluate when their combination is beneficial during peripheral and central VA ECMO.

Model-guided gene circuit design for engineering genetically stable cell populations in diverse applications

This paper designs a biomolecular controller to reduce mutation spread in engineered cell populations by linking mutant growth to circuit design parameters through resource-aware modeling.

Systematic bias in malaria parasite relatedness estimation

This paper identifies systematic biases in malaria parasite relatedness estimation and proposes practical tools to address them.

Inferring active and passive mechanical drivers of epithelial convergent extension

This study uses simulations and live cell imaging to distinguish active and passive mechanical drivers of convergent extension in developing tissues.

Accurate Characterization of the Allosteric Energy Landscapes, Binding Hotspots and Long-Range Communications for KRAS Complexes with Effector Proteins : Integrative Approach Using Microsecond Molecular Dynamics, Deep Mutational Scanning of Binding Energetics and Allosteric Network Modeling

This study integrates molecular dynamics, mutational scanning, and network modeling to characterize KRAS-RAF1 binding hotspots, allostery, and conformational dynamics, revealing how oncogenic mutations alter binding affinity and signaling.

Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning

This paper introduces LIgO, a software suite that simulates adaptive immune receptor repertoires with immune information to aid in developing and benchmarking AIRR machine learning methods.

Evaluating genotyping strategies for a small managed population with simulation

This paper evaluates genotyping strategies for a service dog population using simulation, finding that low-pass sequencing outperforms SNP arrays in imputation accuracy and cost-effectiveness.

Apparent timescaling of fossil diversification rates is caused by sampling bias

This study shows that apparent negative scaling between diversification rates and time in fossils is caused by sampling bias, not real evolutionary trends.

Characterizing homology-induced data leakage and memorization in genome-trained sequence models

This paper identifies homology-induced data leakage in genome-trained sequence models and introduces hashFrag to improve evaluation and generalizability.

Multifaceted Actions of Neurosteroids

The paper investigates the range of actions of neurosteroid analogues using in silico and in vitro methods, revealing unexpected modulation of multiple targets beyond GABA-A receptors.

Reducing maladaptive behavior in neuropsychiatric disorders using network modification

This paper demonstrates a computational approach to reduce maladaptive behavior in neuropsychiatric disorders by modifying neural networks in a model of alcohol drinking.

DeepFocus: A Transnasal Approach for Optimized Deep Brain Stimulation of Reward Circuit Nodes

DeepFocus optimizes deep brain stimulation for reward circuit nodes using transnasal electrodes and simulation, achieving focal fields comparable to established thresholds.

Polarity sorting of actin filaments by motor-driven cargo transport

This study shows that motor-driven cargo transport can sort actin filaments into polarity domains separated by cargo clusters, with effects influenced by cargo number, motor density, and filament length.

Episodic and associative memory from spatial scaffolds in the hippocampus

This paper introduces a neural network model of the hippocampus that integrates spatial and episodic memory by using structured scaffold states for high-capacity, error-correcting memory storage.

Self-organized and self-sustained ensemble activity patterns in simulation of mouse primary motor cortex

The paper simulates mouse primary motor cortex activity and finds self-organized, self-sustained avalanches with power-law distributions in size and duration.

Optimization of a maize rapid cycle breeding scheme using the Modular Breeding Program Simulator (MoBPS)

The paper uses stochastic simulations to optimize a maize breeding scheme by balancing genetic gains and diversity through additional phenotyping and external genetic material.

Skin hydration by natural moisturizing factors, a story of H-bond networking

This study investigates the role of natural moisturizing factors in skin hydration through molecular dynamics simulations, showing their impact on lipid diffusion and membrane properties.

Improved Functional Classification of Hydrolases through Pairwise Structural Similarity of Reaction Cores

The paper develops a method to classify hydrolase functions using structural similarity of reaction cores, identifying enzyme backbones that can support multiple catalytic activities.

Strategies to improve selection compared to selection based on estimated breeding values

The paper compares selection strategies to improve genetic gain and reduce inbreeding over multiple generations using simulation software.

Robustness of Selection and Timing Inference under Model Variation in Population Genetics

This paper analyzes how model mismatches affect the inference of selection coefficients and mutation timing in population genetics, showing that time of onset is sensitive to assumptions about reproductive variance and generations.

Harnessing Computational Insights to Identify Potent Inhibitors for Human Metapneumovirus (HMPV): A Synergistic Approach with Natural Compounds

This study identifies natural compounds as potential inhibitors of HMPV matrix protein through computational screening and analysis.