Lennard-Jones Potential Research Articles

A model for the interaction of a pathogen and an innovative antimicrobial nanocoating

AbstractIn the ongoing battle against infectious diseases, innovative nanotextured antipathogenic coatings provide promising avenues for preventing pathogens from spreading. Understanding their interactions at the micro/nanoscale is crucial for improving their design and efficacy. This work proposes a model for the interaction between pathogens and nanotextured antipathogenic coated surfaces. For this purpose, the forces and deformations experienced by pathogens upon contact with nanotextured surfaces are studied. To achieve this goal, a computational model based on the molecular dynamics software ESPResSo and, particularly, the Object-In-Fluid implementation, has been developed, extending the previous works of I. Jančigova et al. and G. Lazzini et al. More specifically, a Staphylococcus Aureus bacterium is modelled as an elastic cell represented by a triangular mesh and immersed in a computational Lattice-Boltzmann fluid. The size, shape and elastic properties of the pathogen cell are tuned, emulating those of Staphylococcus Aureus. A poly(methyl methacrylate) substrate laser-sintered with Ag nanoparticles is modelled with a triangular mesh, and the interactions between the cell and the substrate are introduced through a Lennard-Jones potential. The simulations performed reveal the influence of surface geometry and dispersion in the coated substrate, providing critical insights into designing more effective antibacterial surfaces that inhibit pathogen proliferation.

Effect of doping on suppression of Coulomb explosion in dicationic noble gas clusters

Dicationic noble gas clusters undergo disintegration due to the repulsive force between charged ions, known as Coulomb explosion (CE). However, beyond a certain size limit, the attractive forces suppress the Coulombic repulsion, enabling the clusters to stabilise. We explored the potential energy surface (PES), which incorporates electrostatic interactions (including Coulombic and induced dipole) and the Lennard-Jones potential, using parallel tempering to determine the cutoff limit for suppressing Coulomb explosions (CE) in both pure and doped noble gas clusters. The influence of both homogeneous (i.e. both charge on two bigger atoms) and heterogeneous charge distributions (i.e. two units of charge being centred on one large and one smaller atom) is evaluated for doping applications. The simulations reveal that single ion ejection is the major dissociation pathway below the cutoff limit. Additionally, the cutoff limit smoothly decreases with gradual doping of heavier atoms in both types of charge distribution.

Feller and ergodic properties of jump–move processes with applications to interacting particle systems

Abstract We consider Markov processes that alternate continuous motions and jumps in a general locally compact Polish space. Starting from a mechanistic construction, a first contribution of this article is to provide conditions on the dynamics so that the associated transition kernel forms a Feller semigroup, and to deduce the corresponding infinitesimal generator. As a second contribution, we investigate the ergodic properties in the special case where the jumps consist of births and deaths, a situation observed in several applications including epidemiology, ecology, and microbiology. Based on a coupling argument, we obtain conditions for convergence to a stationary measure with a geometric rate of convergence. Throughout the article, we illustrate our results using general examples of systems of interacting particles in $\mathbb{R}^d$ with births and deaths. We show that in some cases the stationary measure can be made explicit and corresponds to a Gibbs measure on a compact subset of $\mathbb{R}^d$ . Our examples include in particular Gibbs measures associated to repulsive Lennard-Jones potentials and to Riesz potentials.

Effect of Temperature on Adsorption Behavior and Micromechanical Mechanism Between Graphene and Benzene

Graphene, as a drug carrier material that has been widely concerned in recent years, plays an important role in the delivery system of benzene-containing drug molecules. Combined with atomic force microscope experiment, molecular dynamics simulation and theoretical analysis, the micromechanical mechanism of the influence of temperature on the adsorption or desorption behavior between graphene and benzene was revealed. The results show that the low temperature environment is more favorable to the adsorption of benzene on graphene surface than that of high temperature. The influence of temperature on the Brown effect and the parameters in the Lennard-Jones (6-12) Potential are the two main reasons for this phenomenon. Based on the above conclusions, the Lennard-Jones Temperature-Dependent Potential between monolayer graphene and single benzene was obtained. This is a dynamic balance potential which is different from the static balance of the original potential. The results of this study indicate that controllable adsorption or desorption of drug molecules inside and outside the human body can be achieved by controlling temperature (Low-temperature adsorption in vitro and high-temperature desorption in vivo). This proves that graphene as a drug carrier has strong temperature response characteristics and great application prospects.

Phase Coexistence in Hamiltonian Hybrid Particle-Field Theory Using a Multi-Gaussian Approach.

This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with attractive and steric components analogous to Lennard-Jones (LJ) potentials, which are crucial for modeling phase coexistence. We compare the performance of this method with the multi-Gaussian core model (MGCM) in simulating liquid-gas coexistence for a single-component system across various densities and temperatures. Our results show that HhPF effectively captures detailed information on phase coexistence and interfacial phenomena, including microconfiguration transitions and increased interfacial fluctuations at higher temperatures. Notably, the phase boundaries obtained from HhPF simulations align more closely with those of LJ systems compared to the MGCM results. This work advances the hybrid particle-field methodology to address phase coexistence without requiring modifications to the equation of state or introducing additional interaction energy functional terms, offering a promising approach for mesoscale molecular simulations of complex systems.

Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.

In this work the 4-point polarizable SWM4 Drude water model is reparametrized. Multiple models were developed using different strategies toward reproduction of specific target data. Results indicate that no individual model can reproduce all the selected target data in the context of the present form of the potential energy function. The changes considered in the new models include, 1) variations in the gas phase dipole moment, 2) variations in the molecular polarizability, 3) variations of the distance between the oxygen and the M site, 4) variation of the oxygen Lennard-Jones (LJ) parameters, 5) introduction of a LJ potential to the hydrogen atoms, and 6) variations of the H-O-H angle. Detailed analysis is presented for 3 new water models from which a final model, SWM4-HLJ, is selected as the future default model for the Drude polarizable force field. The model maintains the gas phase dipole moment as the experimental value while the remaining listed terms were adjusted including a larger H-O-H angle (108.12). Compared to its predecessor, SWM4-NDP, the self-diffusion coefficient, water dimer properties, and water cluster energies are greatly improved. The temperature dependence of the density of the new model also performs better. Overall, the new SWM4-HLJ water model is a general improvement and a good balance between microscopic and bulk properties is achieved.

Role of harmonic and anharmonic interactions in controlling the cooperativity of spin-crossover molecular crystals

We present a theoretical model of spin transitions in homogeneous spin-crossover (SCO) materials, based on the description of the interactions between SCO molecules by the Lennard-Jones potential in which the equilibrium distances depend on the spin states of the linked molecules. By expanding the potential to order 3 considering a homogeneous lattice spacing, we demonstrate that the present model is isomorphic with an Ising-like model combining infinite long-range “ferromagnetic-like” interactions, competing with short-range “antiferromagnetic-like” between nearest neighbors in the case of harmonic interactions. When an anharmonic contribution is included, the short-range interaction becomes dependent on the average high-spin fraction, and changes its sign along the spin transition. The thermodynamic properties of the model were first investigated analytically in mean field approximation for both harmonic and anharmonic cases, for which we clarify the conditions for obtaining gradual and first-order transitions. Moreover, we demonstrated that within this approximation, the strength of the antiferromagnetic-like interactions are insufficient to produce multistep transitions. In contrast, the resolution of the previous emerging Ising-like model by Monte Carlo simulations demonstrated the possibility of obtaining gradual, first-order and two-step transitions as a result of the antagonism between long- and short-range interactions. Overall, the obtained results demonstrate the suitability of the present theoretical model to describe cooperative SCO materials. The key message of our paper is that our model can be used to predict complex behavior of spin-crossover crystals. Published by the American Physical Society 2024

Effects of interfacial imperfections on nanoscale adhesive contact for layered medium

Depending on processing technologies and working conditions, imperfect bonding at the layer-substrate interface may occur, resulting in diverse mechanical responses compared to a perfectly bonded layer-substrate system. This study focuses on an imperfect interface under force-like conditions and incorporates it into a nanoscale adhesive contact model to explore the influences of interfacial imperfection on the adhesive contact behaviors of the layered medium. The adhesive contact model is formulated based on the Lennard-Jones (LJ) potential and the Hammaker summation method. The adhesive contact problem is addressed by solving the nonlinear surface gap equations between the contact bodies. The deformation within the gap equations, accounting for the influence of imperfections, is computed using the fast Fourier transform (FFT) algorithm. This study explores the influence of three stress jumping coefficients t1, t2 and t3, which quantitatively characterize the interfacial imperfection, and their coeffects with material parameters, including imperfection depth (layer thickness), adhesion work, and elastic modulus, on the adhesive contact behaviors of the layered medium. The findings underscore that the normal stress jumping coefficient t3 exerts the most significant impact, wherein a higher t3 value corresponds to a smaller adhesive force and a larger absolute contact approach, while tangential stress jumping coefficients t1 and t2 exhibit negligible influence. Decreasing t3 values correspond to varying interaction force-contact approach responses and contribute to alleviating contact stability in cases with large Tabor parameters. Interfacial imperfections manifest their influence by modifying the pressure-displacement response, with noticeable effects only within a specific imperfection depth range h¯<40. While the introduction of interfacial imperfections does not alter the fundamental impact of material parameters—such as imperfection depth, adhesion work ratios, and elastic modulus ratios—on adhesive force and contact approach, it does modify the magnitude of these effects. Furthermore, imperfections alter stress distribution, increasing maximal von Mises stress and causing stress concentration within the layer and at the interface. In summary, force-like imperfections reduce surface displacement, resulting in a smaller region of positive pressure and ultimately contributing to a larger adhesive force. However, this effect is accompanied by increased stress concentration at the imperfect interface. This heightened stress level poses a potential risk to the system's reliability.

Numerical analysis of molecular vibration under Lennard-Jones potential

Numerical analysis of molecular vibration under Lennard-Jones potential

Effect of pores and moisture on the mechanical properties of calcium silicate hydrate gels at mesoscale

Pores and moisture significantly influence the mechanical properties of cementitious materials. Investigating the effects of pores and moisture on the mechanical properties of calcium silicate hydrate (C-S-H) gels at the mesoscale is fundamental to understanding the multiscale behavior of these materials. In this study, mesoscopic models of C-S-H gels with varying porosities were developed using coarse-grained C-S-H nanoparticles. The potential function, describing the interaction between C-S-H nanoparticles under different humidity conditions, was derived based on the mechanical properties of C-S-H nanoparticles, the Lennard-Jones (LJ) potential, and capillary theory. Subsequently, simulations of uniaxial tensile, uniaxial compression, and shear experiments on C-S-H gels with different porosities and moisture levels were conducted. The influence of pores and moisture on the mechanical properties of C-S-H gels was analyzed using two-way analysis of variance (ANOVA) and then compared with mesoscopic influence patterns. The results showed that the mechanical properties of C-S-H gels decrease with increasing porosity and moisture at the mesoscale. And there is an interaction effect between gel pore porosity and moisture. The smaller the porosity, the more significant the weakening effect of increasing moisture on elastic parameters and strength. Conversely, the weakening effect of increasing porosity on elastic parameters and strength is more significant at lower moisture levels. The interaction between pores and moisture has a more pronounced effect on strength, which intensifies with increased moisture. The effect of porosity on the mechanical properties of C-S-H gels is consistent with macroscale studies. However, the effect of moisture on elastic parameters exhibits an opposite trend, attributed to the different mechanisms of water's influence at different scales.

O2/N2 separation via delocalization of the magnetic moment in the TM-CNT nano-magnets array under external magnetic field gradient: A molecular dynamic simulation study

This work presents the design of a new membrane including an array of nano-magnets (magnetic CNTs) as an alternative candidate for efficient O2/N2 separation by using the molecular dynamics (MD) technique. The behavior of the magnetic CNTs is based on the delocalized magnetic moments of transition metal elements which embedded within the CNTs. Hence, the magnetic membrane technology is employed together with the magnetic separation technology for O2/N2 separation; Different responses of paramagnetic oxygen and diamagnetic nitrogen molecules under an applied magnetic field gradient are the basis of the performance of this system. Permeability and selectivity of the membrane are investigated through the involvement of magnetic dipole–dipole and pare-particle Lennard-Jones (L-J) interactions in a constant gas pressure difference on the sides of the membrane. The effects of the multilayering and other design parameters (interlayer distance d, interablock spacing ℓ, slit size s) on the separation performance of MCNTM are investigated. It was found that the separation performance is sensitive to variations in d, ℓ, and s. Furthermore, the influence of the strong or weak magnetic gradient rate and also the temperature are evaluated numerically. Finally, this work provides computational evidence that the magnetic multilayer MCNTM can be used as a high-performance O2/N2 separator, as well as, an oxygen buffer or a temporary storage system at room temperature and 77 K.

Effects of Confinement on Potential Wavelength in Doubly Eccentric Quantum Dot Structures with a Modified Lennard-Jones Potential

Effects of Confinement on Potential Wavelength in Doubly Eccentric Quantum Dot Structures with a Modified Lennard-Jones Potential

Molecular dynamics study of the scratching property of the tetrahedral amorphous carbon coating on the piston ring

In order to reduce friction and wear of the piston ring-cylinder liner system of the internal combustion engine, the tetrahedral amorphous carbon (ta-C) coating on the piston ring is considered. The scratching properties of the ta-C coating and diamond ball are studied by molecular dynamics simulation. The atomic configuration, surface morphology, RMS roughness, friction force, coefficient of friction, wear rate, and normal stress of the ta-C coating are analysed under different scratching depths, substrate temperatures, and scratching velocities. The interatomic interactions are described using the second nearest-neighbour modified embedded-atom method potential, as well as Tersoff potential and Lennard-Jones potential. The simulation results show that the ta-C coating exhibits excellent scratching properties. The scratching depth has a significant effect on the scratching property of the ta-C coating, while the substrate temperature and scratching velocity have a relatively small effect.

Coarse-Grained MD Simulations of the Capillary Interaction between a Sphere and a Binary Fluid with Truncated Lennard-Jones Potentials.

In atomic force microscopy experiments on fluid samples, a capillary bridge forms between the tip and the fluid, causing an attractive capillary force. Here, we present a computational model of the capillary interaction between a solid sphere and a coarse-grained Lennard-Jones fluid containing 10% antifreeze particles with an enlarged van der Waals radius. The capillary force acting on the sphere is obtained from the displacement of the sphere in a trap potential as the sphere is incrementally approached and then retracted from the fluid. This yields force-distance data similar to that obtained in atomic force microscopy experiments. We use this methodology to study the influence of the cutoff radius of the truncated Lennard-Jones potentials on the capillary force and its temperature dependence. The latter is found to scale with the critical temperature of the system. With the presented approach, the tip-sample interaction can be studied for a wide range of complex fluids, particle shapes, and force-probing schemes.

Multidomain Protein-Urea Interactions: Differences in Binding Behavior Lead to Different Destabilization Tendencies for Monoclonal Antibodies.

We study the influence of urea on the stability of monoclonal antibodies (mAbs) using molecular dynamics (MD) simulations in combination with differential scanning fluorimetry (DSF). We show that a denaturing cosolute such as urea binds strongly to the protein, which can lead to denaturation and enhanced aggregation behavior at high temperatures. The interaction between protein and urea crucially depends on the surface properties of the individual mAb domains and therefore affects the general binding to the protein differently. The study of these mechanisms for proteins with multiple domains, such as mAbs, encounters significant limitations in experimental analysis methods due to their complexity. Using computational and experimental methods, we are able to separate the protein-urea interaction by domain and show that Lennard-Jones interactions are mainly responsible for significant binding effects. Our results emphasize the potential of MD simulations in combination with Kirkwood-Buff theory to study the interactions between proteins with multiple domains and cosolutes as formulation excipients for drug discovery and development.

Rejection of heavy metal ions in water by zeolite forward osmosis membrane

Water treatment of heavy metals using zeolite membranes in forward osmosis was demonstrated. A continuous Na-ZSM-5, aluminosilicate zeolite, crystal layer was synthesized on the outer surface of a porous tubular α-alumina support and used as the forward osmosis membrane. The rejection performances and fouling resistances of Na-ZSM-5 membrane were studied. Na-ZSM-5 membrane exhibited a high rejection performance of 99 % for various metal species (As(III), As(V), Se(IV), Se(VI), Cr(VI)). This superior rejection performance was achieved by combining the molecular sieving effect and electrostatic repulsion between the anions and the anionic framework of the zeolite. Na-ZSM-5 membrane exhibited a stable water flux in the presence of model foulants such as sodium alginate, humic acid, bovine serum albumin, and silica particles, suggesting that the membrane had excellent antifouling properties against both organic and inorganic foulants.

Evaluation of the Second Virial Coefficient for the Mie Potential Using the Method of Brackets

The second virial coefficient for the Mie potential is evaluated using the method of brackets. This method converts a definite integral into a series in the parameters of the problem, in this case this is the temperature T. The results obtained here are consistent with some known special cases, such as the Lenard-Jones potential. The asymptotic properties of the second virial coefficient in molecular thermodynamic systems and complex fluid modeling are described in the limiting cases of T → 0 and T → ∞ .

Hysteresis resulting from Lennard–Jones interactions

Hysteresis resulting from Lennard–Jones interactions

Constitutive modelling for understanding stress-stretch behaviour of Lennard-Jones non-crystalline molecular Solid

Abstract Non-crystalline molecular solid materials have many scientific and engineering applications. This study develops a constitutive equation for understanding stress-stretch behaviour of non-crystalline molecular solid using Lennard-Jones (LJ) intermolecular interaction. The strain energy derived from Lennard-Jones interactions between molecules. Based on the excluded volume (spherical volume occupied by the molecules maintaining centre to centre distance with a reference molecule) and density of the molecules, strain energy density is developed. In order to relate the molecular approach with continuum approximation, the excluded volume and density are expressed as a function of strain invariants of right Cauchy-Green deformation tensor. Finally, the constitutive equation in the form of Cauchy stress tensor is developed using the present strain energy density function. The present constitutive model is used to study finite deformations of the molecular solid like uniaxial extension. We compare our theoretical results with the experimental data of flexible polyurethane foams and obtain very good agreements. The current constitutive model can predict the deformation of micro/nano engineering system components.

Charge regulated pH/NIR dual responsive nanoplatforms centered on cuproptosis for enhanced cancer theranostics

Multifunctional nanoplatforms capable of simultaneously executing multimodal therapy and imaging functions are of great potentials for cancer theranostics. We present an elegantly designed, easy-to-fabricate poly(acrylic acid)/mesoporous calcium phosphate/mesoporous copper phosphate nanosphere (PAA/mCaP/mCuP NS) with outstanding pH/NIR-sensitive multimodal-synergic anti-tumor effects. Optimal porous PAA NS scaffolds were prepared at room temperature by balancing the intra-PAA polymer and polymer-solvents Lennard-Jones potentials in a water:isopropyl alcohol (IPA) mix-solvent. Subsequent sponging of Ca2+ and Cu2+, and adsorption of PO43− to the PAA template were achieved through exquisite electrostatic interactions among ions and the ionizable PAA side-chain in an aqueous environment. This forms the basis for the tumor microenvironment pH-triggered release of Cu2+ to induce cuproptosis, as well as the photothermal effect originating from CuP, while Ca2+ can enhance the nanoplatform's biocompatibility and can damage mitochondria when overloaded. Lastly, PAA/mCaP/mCuP NSs still exhibit high drug loading efficiency for doxorubicin (DOX), enabling chemotherapy. Satisfactory anti-tumor effects of these modalities, along with their synergistic effects, were verified both in vitro and in vivo, with the NSs demonstrating good biodegradation in the latter. The fabricated NS itself holds great promise as an anti-tumor nanomedicine, and the thorough mechanical insights into NS formation may inspire the design of next-generation multifunctional nanoplatforms.