Research Articles
Convergence Challenges in Long MD Simulations: Understanding and Optimizing Diffusion Analysis for Biomolecular Research
This article addresses the critical yet often overlooked challenge of achieving convergence in long-scale Molecular Dynamics (MD) simulations, with a specific focus on diffusion processes critical for drug development and...
Improving Statistical Accuracy in Diffusion Coefficient Calculation: A Guide for Biomedical Researchers
This article provides a comprehensive guide for researchers and drug development professionals on improving the statistical rigor and reliability of diffusion coefficient calculations.
Nonlinear MSD Curves: Decoding Anomalous Diffusion for Drug Delivery and Biomaterial Research
This article addresses the common challenge of nonlinear mean squared displacement (MSD) curves in single-particle tracking and diffusion studies, a key issue for researchers characterizing nanoparticle motion in complex biological...
A Comprehensive Guide to Trajectory Analysis Tools for Mean Squared Displacement in Biomedical Research
This article provides researchers, scientists, and drug development professionals with a comprehensive overview of Mean Squared Displacement (MSD) analysis for single-particle trajectories.
Calculating Diffusion Coefficients with ReaxFF MD: A Comprehensive Tutorial from Fundamentals to Advanced Applications
This tutorial provides a comprehensive guide for researchers and scientists on calculating diffusion coefficients using ReaxFF molecular dynamics.
Benchmarking the GAFF Force Field: A Practical Guide for Predicting Molecular Diffusion in Drug Development
Accurate prediction of molecular diffusion coefficients is critical for modeling drug solubility, membrane permeability, and binding kinetics.
Temperature-Dependent Diffusion Coefficients: From Arrhenius Theory to Molecular Dynamics Validation in Biomedical Research
This article provides a comprehensive guide for researchers and drug development professionals on utilizing Arrhenius plots and Molecular Dynamics (MD) simulations to study temperature-dependent diffusion coefficients.
Unwrapping Coordinates for Correct Diffusion Calculation: Methods and Applications in Biomedical Research
Accurate analysis of diffusion processes is pivotal in biomedical research, from understanding single-molecule dynamics in cells to optimizing drug delivery systems.
Finite-Size Effects Correction in Molecular Dynamics: A Comprehensive Guide to Accurate Diffusion Coefficients
This article provides a systematic examination of finite-size effects on diffusion coefficients computed from molecular dynamics simulations, addressing self-diffusion, Maxwell-Stefan, and Fick diffusion coefficients across pure fluids to multicomponent mixtures.
Multiple Short vs. Single Long MD Trajectories: A Strategic Guide for Enhanced Sampling in Biomedical Research
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structure and dynamics, critical for applications in drug discovery.