Comparison of Force Fields for the Prediction of Thermophysical Properties of Long Linear and Branched Alkanes

Cholesterol-ester prevents lipoprotein core from solidifying: Molecular dynamics simulation

As an important part of lipid metabolism the liver produces large particles called very low density lipoproteins, filled mostly with triglyceride and cholesterol esters mixture. A large percentage of the mixture composition components has a melting point above physiological temperature. Thus solid cluster formation or phase transition could be expected. Though various single-component triglyceride systems are well researched both experimentally and by various simulation techniques, to our best knowledge, tripalmitin/cholesteryl-palmitate binary mixture was not yet studied. We study tripalmitin single component system, as well as 20%-80% and 50%-50% binary mixtures of cholesteryl-palmitate and tripalmitin using molecular dynamics approach. All systems are studied at the pressure of 1 atm and the physiological temperature of 310 K, which is below the melting points of both tripalmitin and cholesteryl-palmitate. Our results show that at the time of 1000 ns, there is still no phase transition, but there is a noticeable tendency to intermolecular organizing and early signs of clustering. We check fatty acid arrangements of tripalmitin molecules in both single component system and binary mixtures with two different percentages of cholesteryl-palmitate mixed in. Our results show that the more cholesteryl-palmitate molecules are in the mixture the smaller number of tripalmitin molecules transitions to 'a fork/chair' configuration during the same calculation time. Calculated angle distributions between fatty acid chains of tripalmitin molecules confirm that. Thus, our simulation results suggest slowing down or interfering effect of cholesteryl-palmitate on the crystallizing process of the binary mixture.

Dynamical properties of hydrogen fluid at high pressures

The properties of the hydrogen fluid at high pressures are still of interest to the scientific community. The experimentally unreachable dynamical properties could provide new insights into this field. In 2020 [Cheng et al., Nature 585, 217-220 (2020)], the machine-learned approach allows the calculation of the self-diffusion coefficient in the warm dense hydrogen with higher precision. After that, the work [van de Bund et al., Phys. Rev. Lett. 126(22), 225701 (2021)] reports the ab initio treatment of isotopic effects on diffusion in H2/D2 and a significant increase in its value in the region of the phase transition. Both works indicate the anomalous growth of diffusion, but the reasons for this phenomenon are unclear. In the present work, we reveal the plasma-like behavior of the diffusion growth. We apply the classical molecular dynamics method using a machine learning potential developed on the ab initio modeling for the prediction of diffusion and shear viscosity coefficients. We consider dependencies of the vibrational spectrum, molecule lifetime, diffusion, and shear viscosity coefficients on density along the isotherms in the temperature range from 600 to 1100 K.

Molecular Simulations of Thermal Transport across Iron Oxide-Hydrocarbon Interfaces

The rational design of dielectric fluids for immersion cooling of batteries requires a molecular-level understanding of the heat flow across the battery casing/dielectric fluid interface. Here, we use nonequilibrium molecular dynamics (NEMD) simulations to quantify the interfacial thermal resistance (ITR) between hematite and poly-α-olefin (PAO), which are representative of the outer surface of the steel battery casing and a synthetic hydrocarbon dielectric fluid, respectively. After identifying the most suitable force fields to model the thermal properties of the individual components, we then compared different solid-liquid interaction potentials for the calculation of the ITR. These potentials resulted in a wide range of ITR values (4-21 K m2 GW-1), with stronger solid-liquid interactions leading to lower ITR. The increase in ITR is correlated with an increase in density of the fluid layer closest to the surface. Since the ITR has not been experimentally measured for the hematite/PAO interface, we validate the solid-liquid interaction potential using the work of adhesion calculated using the dry-surface method. The work of adhesion calculations from the simulations were compared to those derived from experimental contact angle measurements for PAO on steel. We find that all of the solid-liquid potentials overestimate the experimental work of adhesion. The experiments and simulations can only be reconciled by further reducing the strength of the interfacial interactions. This suggests some screening of the solid-liquid interactions, which may be due to the presence of an interfacial water layer between PAO and steel in the contact angle experiments. Using the solid-liquid interaction potential that reproduces the experimental work of adhesion, we obtain a higher ITR (33 K m2 GW-1), suggesting inefficient thermal transport. The results of this study demonstrate the potential for NEMD simulations to improve understanding of the nanoscale thermal transport across industrially important interfaces. This study represents an important step toward the rational design of more effective fluids for immersion cooling systems for electric vehicles and other applications where thermal management is of high importance.

Coarse-Grained Simulations of Columnar Ionic Liquid Crystals: Comparison with Experiments

We simulate a homologous series of guanidinium-based columnar ionic liquid crystals (ILCs) using coarse-grained molecular dynamics (MD) simulations with the Martini force field. We systematically vary the length of alkyl side chains, ILC-n (n = 8, 12, 16), and compare our results with previous experimental findings. Experimentally, ILC-8 exhibits a narrow mesophase window and weak columnar order, while ILC-12 and ILC-16 display a broad mesophase window and high columnar order. The MD simulations show that ILC-8 forms a percolated structure, whereas the longer chain analogues self-assemble into columns, with columnar assembly becoming more prominent as the side chain length increases, in qualitative agreement with the experiments. Furthermore, the intercolumnar distance increases monotonically with increasing side chain length and decreases with increasing temperature. Finally, we find that the diffusion coefficient and ionic conductivity decrease substantially with increasing chain length, consistent with experimental observations. We attribute this decrease in mobility to the formation of hexagonally ordered columns, which restrict transport more than percolated networks.

Passive fractionating mechanism for oil spill using shear-wettability modulation

Oil spillage and organic solvent leakage have been a frequent occurrence in recent years, which pose a significant threat not only to the aquatic ecosystems but also result in substantial economic burdens. This has necessitated the search for materials capable of separating oil from water at enhanced efficiency with superior mechanical and thermal properties. In this study, we conduct a set of systematic molecular dynamics simulations to investigate the potential of two-dimensional graphene-like channels under extreme confinement to achieve efficient oil-water separation. Effective modulation of the wetting characteristics of graphene-like surfaces juxtaposed with unconventional flow behavior at the nanoscale unveils differential interaction of water and oil molecules towards the wall, thereby resulting in distinct separation zones for varying compositions of the oil-water mixture. Such separation zones have been observed to be highly correlated with mixture temperature, which provides effective separation pathways across diverse environmental conditions. Our study offers a paradigm shift in oil-water separation strategies, which not only provides deeper insights into the equilibrium and dynamic behavior of a two-phase mixture but also holds immense implications for the development of smart, wettability-based oil separation devices.

Dental biomaterials redefined: molecular docking and dynamics-driven dental resin composite optimization

BACKGROUND

Dental resin-based composites are widely recognized for their aesthetic appeal and adhesive properties, which make them integral to modern restorative dentistry. Despite their advantages, adhesion and biomechanical performance challenges persist, necessitating innovative strategies for improvement. This study addressed the challenges associated with adhesion and biomechanical properties in dental resin-based composites by employing molecular docking and dynamics simulation.

METHODS

Molecular docking assesses the binding energies and provides valuable insights into the interactions between monomers, fillers, and coupling agents. This investigation prioritizes SiO2 and TRIS, considering their consistent influence. Molecular dynamics simulations, executed with the Forcite module and COMPASS II force field, extend the analysis to the mechanical properties of dental composite complexes. The simulations encompassed energy minimization, controlled NVT and NPT ensemble simulations, and equilibration stages. Notably, the molecular dynamics simulations spanned a duration of 50 ns.

RESULTS

SiO2 and TRIS consistently emerged as influential components, showcasing their versatility in promoting solid interactions. A correlation matrix underscores the significant roles of van der Waals and desolvation energies in determining the overall binding energy. Molecular dynamics simulations provide in-depth insights into the mechanical properties of dental composite complexes. HEMA-SiO2-TRIS excelled in stiffness, BisGMA-SiO2-TRIS prevailed in terms of flexural strength, and EBPADMA-SiO2-TRIS offered a balanced combination of mechanical properties.

CONCLUSION

These findings provide valuable insights into optimizing dental composites tailored to diverse clinical requirements. While EBPADMA-SiO2-TRIS demonstrates distinct strengths, this study emphasizes the need for further research. Future investigations should validate the computational findings experimentally and assess the material's response to dynamic environmental factors.

Wettability-modulated behavior of polymers under varying degrees of nano-confinement

Extreme confinement in nanochannels results in unconventional equilibrium and flow behavior of polymers. The underlying flow physics dictating such paradigms remains far from being understood and more so if the confining substrate is composed of two-dimensional materials, such as graphene. In this study, we conducted systematic molecular dynamics simulations to explore the effect of wettability, confinement, and chain length on polymer flow through graphene-like nanochannels. Altering the wetting properties of these membranes that structurally represent graphene results in substantial changes in the behavior of polymers of disparate chain lengths. Longer hydrocarbon chains (n-dodecane) exhibit negligible wettability-dependent structuring in narrower nanochannels compared to shorter chains (n-hexane) culminating in higher average velocities and interfacial slippage of n-dodecane under less wettable conditions. We demonstrate that the wettability compensation comes from chain entanglement attributed to entropic factors. This study reveals a delicate balance between wettability-dependent enthalpy and chain-length-dependent entropy, resulting in a unique nanoscale flow paradigm, thus not only having far-reaching implications in the superior discernment of polymeric flow in sub-micrometer regimes but also potentially revolutionizing various applications in the oil industry, including innovative oil transport, oil extraction, ion transport polymers, and separation membranes.

Extension of the MolMod Database to Transferable Force Fields

MolMod, a web-based database for classical force fields for molecular simulations of fluids [Mol. Sim. 45, 10 (2019), 806-814], was extended to transferable force fields. Eight transferable force fields, including all-atom and united-atom type force fields, were implemented in the MolMod database: OPLS-UA, OPLS-AA, COMPASS, CHARMM, GROMOS, TraPPE, Potoff, and TAMie. These transferable force fields cover a large variety of chemical substance classes. The system is designed such that new transferable force fields can be readily integrated. A graphical user interface was implemented that enables the construction of molecules. The MolMod database compiles the force field for the specified component and force field type and provides the corresponding data and meta data as well as ready-to-use input files for the molecule for different simulation engines. This helps the user to flexibly choose molecular models and integrate them swiftly in their individual workflows, reducing risks of input errors in molecular simulations.

Computation of Shear Viscosity by a Consistent Method in Equilibrium Molecular Dynamics Simulations: Applications to 1-Decene Oligomers

Accurate computation of shear viscosity is fundamental for describing fluid flow and designing and developing new processes. Poly-α-olefins (PAO's), particularly from 1-decene, have been applied to a variety of industrial processes. Recently, these molecules have been applied as carbon dioxide thickeners, enhancing carbon dioxide viscosity, which is important in carbon dioxide injection, either for enhanced oil recovery or sequestration in geological formations. For these applications, knowledge of the pure oligomer viscosity is crucial to design and operate the oligomer upstream pipelines before mixing them with carbon dioxide. Using Green-Kubo formalism with equilibrium molecular dynamics simulations, two methods are presented in the literature to generate the traceless, symmetric pressure tensor. In this work, we show that these two methods provide different values of shear viscosity, from the analysis of how the diagonal components of the traceless, symmetric pressure tensor are computed in each method. Then, we examine the consistency and correctness of each method: one is found to be consistent. The other is corrected by scaling the fluctuations of the diagonal components. Shear viscosities of supercritical carbon dioxide, vapor and liquid n-pentane, and liquid n-decane are computed to illustrate the analysis. We also apply the consistent method to compute the viscosity of 1-decene oligomers, including for the first time larger-than-dimer oligomers (trimer, tetramer, hexamer, and decamer).

Molecular modeling of interfacial properties of the hydrogen + water + decane mixture in three-phase equilibrium

The understanding of interfacial phenomena between H2 and geofluids is of great importance for underground H2 storage, but requires further study. We report the first investigation on the three-phase fluid mixture containing H2, H2O, and n-C10H22. Molecular dynamics simulation and PC-SAFT density gradient theory are employed to estimate the interfacial properties under various conditions (temperature ranges from 298 to 373 K and pressure is up to around 100 MPa). Our results demonstrate that interfacial tensions (IFTs) of the H2-H2O interface in the H2 + H2O + C10H22 three-phase mixture are smaller than IFTs in the H2 + H2O two-phase mixture. This decrement of IFT can be attributed to C10H22 adsorption in the interface. Importantly, H2 accumulates in the H2O-C10H22 interface in the three-phase systems, which leads to weaker increments of IFT with increasing pressure compared to IFTs in the water + C10H22 two-phase mixture. In addition, the IFTs of the H2-C10H22 interface are hardly influenced by H2O due to the limited amount of H2O dissolved in nonaqueous phases. Nevertheless, positive surface excesses of H2O are seen in the H2-C10H22 interfacial region. Furthermore, the values of the spreading coefficient are mostly negative revealing the presence of the three-phase contact for the H2 + H2O + C10H22 mixture under studied conditions.

Structure of the Hexadecane Rotator Phase: Combination of X-ray Spectra and Molecular Dynamics Simulation

Rotator phases are rotationally disordered plastic crystals, some of which can form upon freezing of alkane at alkane-water interfaces. Existing X-ray diffraction studies show only partial unit cell information for rotator phases of some alkanes. This includes the rotator phase of n-hexadecane, which is a transient metastable phase in pure alkane systems, but shows remarkable stability at interfaces when mediated by a surfactant. Here, we combine synchrotron X-ray diffraction data and molecular dynamics (MD) simulations, reporting clear evidence of the face-centered orthorhombic RI rotator phase from spectra for two hexadecane emulsions, one stabilized by Brij C10 and another by Tween 40 surfactants. MD simulations of pure hexadecane use the recently developed Williams 7B force field, which is capable of reproducing crystal-to-rotator phase transitions, and it also predicts the crystal structure of the RI phase. Full unit cell information is obtained by combining unit cell dimensions from synchrotron data and molecular orientations from MD simulations. A unit cell model of the RI phase is produced in the crystallographic information file (CIF) format, with each molecule represented by a superposition of four rotational positions, each with 25% occupancy. Powder diffraction spectra computed using this model are in good agreement with the experimental spectra.

Investigating the Behavior of Various Lubrication Regimes under Dynamic Conditions Using Nonequilibrium Molecular Dynamics

It is crucial to comprehend how the oil film varies under dynamic operating conditions and the accompanying friction properties to better grasp the friction mechanism and control friction behavior. To model the friction characteristics under boundary lubrication (BL) and elastohydrodynamic lubrication (EHL), nonequilibrium molecular dynamics simulations with various numbers of hexadecane molecules as lubricating oil were conducted in this research under the conditions of dynamic speed and dynamic load. All the dynamic operating conditions have the form of sine waves, with various frequencies and amplitudes. According to the findings, the friction force is strongly connected with interfaces where relative sliding takes place, whose number, velocity difference, and the degree of solidification have significant influences. The variation of amplitude under dynamic load can cause a regular change in the density of the lubricating layer, while the variation of frequency can cause a change in molecular layer's range of motion. Both effects are crucial for friction. The structure of the lubricating layer with lower friction varies with various frequencies for dynamic velocity. Both high and small amplitudes of velocity offer advantages to form a stable film structure at low frequencies in the BL and EHL regions, while the amplitude in the BL area has minimal association with friction at high frequencies. At high frequencies in the EHL region, the friction rises as the amplitude of velocity grows and the lubricating layer becomes more unstable.

Data scheme and data format for transferable force fields for molecular simulation

A generalized data scheme for transferable classical force fields used in molecular simulations, i.e. molecular dynamics and Monte Carlo simulation, is presented. The data scheme is implemented in an SQL-based data format. The data scheme and data format is machine readable, re-usable, and interoperable. A transferable force field is a chemical construction plan specifying intermolecular and intramolecular interactions between different types of atoms or different chemical groups and can be used for building a model for a given component. The data scheme proposed in this work (named TUK-FFDat) formalizes digitally these chemical construction plans, i.e. transferable force fields. It can be applied to all-atom as well as united-atom transferable force fields. The general applicability of the data scheme is demonstrated for different types of force fields (TraPPE, OPLS-AA, and Potoff). Furthermore, conversion tools for translating the data scheme between .xls spread sheet format and the SQL-based data format are provided. The data format can readily be integrated in existing workflows, simulation engines, and force field databases as well as for linking such.