Estimating Free-Energy Surfaces and Their Convergence from Multiple, Independent Static and History-Dependent Biased Molecular-Dynamics Simulations with …

A Bjola, M Salvalaglio - Journal of Chemical Theory and …, 2024 - ACS Publications
Addressing the sampling problem is central to obtaining quantitative insight from molecular
dynamics simulations. Adaptive biased sampling methods, such as metadynamics, tackle …

Biomolecular Adsorprion at ZnS nanomaterials: a Molecular Dynamics Simulation Study of the Adsorption preferences, effects of the Surface curvature and coating

R Rahmani, AP Lyubartsev - Nanomaterials, 2023 - mdpi.com
The understanding of interactions between nanomaterials and biological molecules is of
primary importance for biomedical applications of nanomaterials, as well as for the …

Atomistic perspective on biomolecular adsorption on functionalized carbon nanomaterials under ambient conditions

M Saeedimasine, EG Brandt… - The Journal of Physical …, 2020 - ACS Publications
The use of carbon-based nanomaterials is tremendously increasing in various areas of
technological, bioengineering, and biomedical applications. The functionality of carbon …

Protamine binding site on DNA: molecular dynamics simulations and free energy calculations with full atomistic details

A Mukherjee, S Saurabh, E Olive… - The Journal of …, 2021 - ACS Publications
Protamine, an arginine-rich basic protein, compacts DNAs in sperm nuclei to densities
higher than those in somatic cells. The mechanism of this compaction in sperm cells is even …

Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy

L Agosta, L Fiore, N Colozza, G Pérez-Ropero… - Langmuir, 2024 - ACS Publications
We report here an experimental-computational study of hydrated TiO2 anatase
nanoparticles interacting with glycine, where we obtain quantitative agreement of the …

[HTML][HTML] Supercooled liquid-like dynamics in water near a fully hydrated titania surface: Decoupling of rotational and translational diffusion

L Agosta, M Dzugutov, K Hermansson - The Journal of Chemical …, 2021 - pubs.aip.org
We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully
hydrated surface of TiO 2 on the water dynamics. It is found that the universal relation …

Vibrational spectra of human tissues: Experimental data and density functional theory calculations comparison

N Machado, ET Sato, JMR Alape, H Martinho - Vibrational Spectroscopy, 2023 - Elsevier
Biophotonics techniques enabling molecular sensing of tissues and biological samples of
had been widely applied to biomedical problems. Vibrational spectroscopy technologies like …

Adsorption Free Energy of Glycine on TiO2 in Water from First Principles Simulations and Electrochemical Impedance Spectroscopy

L Agosta, L Fiore, N Colozza, A Lyubartsev, F Arduini… - 2021 - researchsquare.com
The adhesion of amino acids and small organic molecules on TiO 2 nanoparticles is
fundamental for bio-nano functionalization of peptides and proteins. The adsorption free …