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Several knowledge gaps on the properties and behavior of hydrogen must be closed to realize its widespread use as a clean fuel and reduction agent. A challenge in this regard is that hydrogen and its mixtures are influenced by quantum effects, in particular at low temperatures. We have implemented new pair potentials into the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) package that semi-classically account for quantum effects. They are called Feynman–Hibbs corrected Mie potentials (Mie–FH) of first and second order. In the literature, these potentials have been shown to accurately represent the thermodynamic properties of hydrogen, deuterium, helium, neon and their mixtures at temperatures above 20 K. We verify the correctness of the LAMMPS implementation by comparing to results from independent Monte Carlo simulations. The computational efficiency of the implementation is assessed for system sizes ranging from several thousands to one billion particles, highlighting the suitability of the implementation for large-scale simulations. The LAMMPS implementation paves the way for new applications, such as studying the transport properties of hydrogen mixtures, or investigating hydrogen confined in porous media.

Stimuli-responsive hydrogels are a class of hydrogels that undergo reversible changes in their physical or chemical properties in response to specific external stimuli. The pH is a critical environmental stimulus for stimuli-responsive hydrogels. When the pH of the surrounding environment changes, it can lead to significant alterations in the properties of the hydrogel, such as swelling behavior, mechanical strength, etc. So, understanding how pH affects the swelling behavior and mechanical properties of these hydrogels is crucial to optimize their performance in biomedical applications. Therefore, in the present study, the effect of pH on the swelling process, mechanical and thermal attributes of polyacrylamide hydrogel structure were studied using molecular dynamics simulation and LAMMPS software. The results reveal that as the pH increased from 2 to 11, the structural volume increased from 342,583 to Å3. The increase in the volume of the structure was in terms of the increase in atomic fluctuations by increasing the pH, and consequently, it led to more swelling. The mechanical properties show that the ultimate strength and Young’s modulus of the sample increase from 0.0298 to 0.0007 to 0.0359 and 0.0012 MPa, respectively. The reason for the increase in these parameters was that by increasing the pH, the attraction force among different components of the PAM hydrogel structure increased. This issue led to an increase in the stability of the nanostructure. Finally, the thermal properties showed that thermal conductivity increased from 0.51 to 0.62 W/m K by increasing pH to 11. The findings may lead to the development of pH-responsive hydrogels with enhanced properties, offering more effective and tailored solutions for biomedical applications.

In this study, the wetting and spreading behavior of AgCuTi ternary alloys on Fe substrate was investigate using a molecular dynamics (MD) modeling method. Modeling indicates that precursor films consisted of single-layer atoms are formed and that the wetting and spreading morphologies of the molten droplets on various crystal surfaces are distinct. Diffusive processes play a key role in the formation of the precursor film, and the droplet spreading morphology is correlated critically with the atomic arrangement of the substrate. The droplet spreading process can be divided into two stages of rapid and slow spreading, and there is an obvious interdiffusion phenomenon close to the solid-liquid contact line. The rate at which droplets spread quickens as the temperature rises. Furthermore, the spreading and diffusion capacities of various elements vary, and these properties are closely related to their chemical reactivity.

The main uses of bullets are as projectiles in firearms for military, law enforcement, and civilian purposes. However, bullets have significant industrial applications beyond their role in weaponry, such as precision drilling, cutting, and shaping of hard materials. Steel bullets have a very resistant structure and will not be damaged if exposed to corrosion. Other applications that are resistant to strike and projectiles, such as the automotive and aerospace industries, are based on fibers or fabrics with high toughness and tensile strength, such as Kevlar and p -aramid fibers, which are impregnated with some thermoplastic or thermoset polymers. Therefore, in the upcoming research, the impact of external force (EF) with various values (0.1, 0.2, 0.3, 0.4, and 0.5 V/Å) on the strength of Kevlar nanofibers reinforced with silicon dioxide (SiO2) nanoparticles and ethylene glycol (EG) has been investigated using LAMMPS software. EG and SiO2 nanoparticles with 10 and 2 vol% were added to Kevlar fabrics, creating a shear thickening fluid (STF) nanocomposite. The energy parameters of the interaction between the particles, collision velocity, and the center of mass have been calculated. The findings of the research indicate an increase in the interaction energy from 111271.85 to 154351.15 kcal/mol, an increase in the collision velocity from 0.7046 to 1.5812 Å/fs and an increase in the center of mass from 0.62671 to 1.1670 Å due to the EF applied from 0.2 to 0.4 (kcal/mol)/Å. These results show EF should be optimized in actual cases for the collision process to occur effectively.

Aerogels are formed from a lattice of interconnected nanoparticles with a nanometer space between them. These nanostructured materials, with very low density and high specific surfaces, show exceptional properties, so their applications in various fields are expanding. In the present study, the mechanical behavior of paraffin-reinforced silica aerogel was examined by the change in the stress-strain curve, ultimate strength (US), and Young's modulus (YM) at different initial temperatures of 300, 310, 320, 330, and 350 K by MD and LAMMPS. It is revealed that rising the initial temperature can affect the silica aerogel's mechanical properties and impair the structure's mechanical strength. By increasing the initial temperature from 300 to 350 K, the US and YM modules declined from 410.45 to 1073.13 to 351.36–661.4 MPa, respectively. Physically, this mechanical performance results from increased atomic oscillations inside the computational box. Therefore, it is concluded that the effect of temperature on silica's mechanical performance is important and used in various industries.

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the Jeffery orbits of an ellipsoid particle in shear flow, red blood cell stretching test, and effective blood viscosity flowing in tubes. It demonstrated essentially linear scaling from 512 to 8192 cores for both strong and weak scaling cases. The computing time for the coupling increased with the solid fraction. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code.