Our recently developed optimized potentials for liquid simulations-virtual site ionic liquid (OPLS-VSIL) force field has been shown to provide accurate bulk phase properties and local ion-ion interactions for a wide variety of imidazolium-based ionic...
Poly(ethylene oxide) (PEO)-based polymers are common hosts in solid polymer electrolytes (SPEs) for high-power energy devices. Molecular simulations have provided valuable molecular insights into structures and ion transport mechanisms of PEO-based S...
Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients (
The transition to sustainable aviation fuel (SAF) is critical for reducing the carbon footprint of the aviation sector while ensuring compatibility with current engines and infrastructure. Regulatory constraints, such as ASTM D7566, currently limit S...
Polyimides feature a vast number of industrial applications due to their high thermal stability and insulation properties. These polymers exhibit an exceptional combination of thermal stability and mechanical toughness, which allows the semiconductor...
Accurately calculating the entropy of liquids is an important goal, given that many processes take place in the liquid phase. Of almost equal importance is understanding the values obtained. However, there are few methods that can calculate the entro...
n-Octanol and related ether alcohols are studied via molecular dynamics (MD) simulations using the two classical all-atom force fields OPLS-AA and CHARMM. The ether alcohols studied possess one ether functionality separated by varying n carbon atoms...
Polyethylene glycol (PEG) is one of the environmentally benign solvent options for green chemistry. It readily absorbs water when exposed to the atmosphere. The Molecular Dynamics (MD) simulations of PEG200, a commercial mixture of low molecular weig...
The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28) peptide in aqueous solution. Moreover, the structural character of Aβ (12–28) peptide is compared with other amylo...
In the past few years, the sol-gel polycondensation technique has been increasingly employed with great success as an alternative approach to the preparation of molecularly imprinted materials (MIMs). The main aim of this study was to study, through...
Cellulose nanofiber (CNF) exhibits excellent mechanical properties, which has been extensively proven through experimental techniques. However, understanding the mechanisms and the inherent structural behavior of cellulose is important in its vastly...
Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding...
In this work, we aim to understand and predict the thermal properties of automotive lubricants using non-equilibrium molecular dynamics. After a previous study on model materials for the mechanical parts of a car engine, we now focus on the thermal c...
For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dyn...
Polyethylene vanillic (PEV), a bio-based material, has mechanical and thermal properties similar to polyethylene terephthalate (PET), the most common polymer used in industries. The present study aimed to investigate and compare their structural dyna...
The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model syste...
Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solutio...
Molecular dynamics (MD) simulations were performed on sterically hindered -conidendrin-based chiral 1,4-diols (LIGNOLs) from the naturally occurring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the...
Polychlorinated dibenzo-p-dioxins (PCDD) are persistent organic pollutants which result as byproducts in industrial or combustion processes and induce toxicity in both wildlife and humans. In this study, all seven PCDD, tetrachlorinated dibenzo-p-dio...
Molecular dynamics (MD) simulations provide a physics-based approach to understanding protein structure and dynamics. Here, we used this intriguing tool to validate the experimental structural model of Hyp-1, a pathogenesis-related class 10 (PR-10) p...
Self-assembled cyclic peptide nanotubes with alternating D- and L-amino acid residues in the sequence of each subunit have attracted a great deal of attention due to their potential for new nanotechnology and biomedical applications, mainly in the fi...
Thermal conductivities of polybutadiene crosslinked with sulfur as a function of the heat flux autocorrelation function by using an equilibrium molecular dynamic (EMD) simulation were investigated. The Green–Kubo method was used to calculate th...
Polyisoprene, with a high degree of polymerization, is the main component of natural rubber. In the industrial production process, it is necessary to adjust the length of the macromolecule of polyisoprene to improve its plasticity. It is thus of vita...
Glucosinolates are secondary plant metabolites of Brassicaceae. They exert their effect after enzymatic hydrolysis to yield aglycones, which become nitriles and epithionitriles through the action of epithiospecifier (ESP) and nitrile-specifier protei...
Our work concerns the study of four candidate drug compounds of the terpenoid family, found as essential oil ingredients in species of the Greek endemic flora, namely carvacrol, p-cymene, γ-terpinene, and thymol, via the simulation method of mo...
The emerging interest in the field of coordination chemistry and their biological applications has created a novel impact in the field of chemical biology. With this motivation, in this work we have synthesized a novel benzimidazole derived imine lig...
Background/Objectives: Tegoprazan (TPZ) is a potassium-competitive acid blocker (P-CAB) used to treat conditions such as gastroesophageal reflux disease, peptic ulcer, and Helicobacter pylori infection. It exists in three solid forms: amorphous, Poly...