Lennard-Jones Research Articles

Influence of cutoff radius and tip atomic structure on energy barriers encountered during AFM tip sliding on 2D monolayers

In computational studies using the Lennard–Jones (LJ) potential, the widely adopted 2.5 σ cutoff radius effectively truncates pairwise interactions across diverse systems (Santra et al 2008 J. Chem. Phys. 129 234704, Chen and Gao 2021 Friction 9 502–12, Bolintineanu et al 2014 Part. Mech. 1 321–56, Takahiro and Kazuhiro 2010 J. Phys.: Conf. Ser. 215 012123, Zhou et al 2016 Fuel 180 718–26, Toxvaerd and Dyre 2011 J. Chem. Phys. 134 081102, Toxvaerd and Dyre 2011 J. Chem. Phys. 134 081102). Here, we assess its adequacy in determining energy barriers encountered by a Si monoatomic tip sliding on various two-dimensional (2D) monolayers, which is crucial for understanding nanoscale friction. Our findings emphasize the necessity of a cutoff radius of at least 3.5 σ to achieve energy barrier values exceeding 95% accuracy across all studied 2D monolayers. Specifically, 3.5 σ corresponds to 12.70 Å in graphene, 12.99 Å in MoS2 and 13.25 Å in MoSe2. The barrier values calculated using this cutoff support previous experiments comparing friction between different orientations of graphene and between graphene and MoS2 (Almeida et al 2016 Sci. Rep. 6 31569, Zhang et al 2014 Sci. China 57 663–7). Furthermore, we demonstrate the applicability of the 3.5 σ cutoff for graphene on an Au substrate and bilayer graphene. Additionally, we investigate how the atomic configuration of the tip influences the energy barrier, finding a nearly threefold increase in the barrier along the zigzag direction of graphene when using a Si(001) tip composed of seven Si atoms compared to a monoatomic Si tip.

Helmholtz energy models for dipole interactions: Review and comprehensive assessment

Dipolar interactions play an important role for thermodynamic properties of many fluids and accordingly for their modeling. In molecular-based equation of state models, the effect of dipolar interactions is usually described by Helmholtz energy models. There are several Helmholtz energy models for dipolar interactions available in the literature today. In this work, eight dipole contribution models describing the dipole–dipole interactions of fluids were critically assessed by comparing their results with molecular simulation reference data of Stockmayer fluids. Therefore, the dipole contribution models were combined with an accurate Lennard-Jones (LJ) Helmholtz energy model. The following thermodynamic properties were considered in the comparison: vapor pressure, saturated densities, enthalpy of vaporization, surface tension (by using density gradient theory), critical point, second virial coefficient, and thermodynamic properties at homogeneous state points, such as the Helmholtz energy, pressure, chemical potential, internal energy, isochoric heat capacity, isobaric heat capacity, thermal expansion coefficient, isothermal compressibility, thermal pressure coefficient, speed of sound, Joule–Thomson coefficient, and Grüneisen parameter. For the evaluation of the dipole contribution models, molecular simulations for the Stockmayer fluid with the dipole moments of μ2/4πϵ0ɛσ3=0.5,1,2,3,4,5 were carried out. The results indicate, that all considered dipole models exhibit some significant weaknesses. Nevertheless, some dipole contribution models are found to provide a robust description for many properties and state ranges. Overall, the deviations of the dipole contribution models from the Stockmayer simulation data are, in most cases, an order of magnitude higher than the deviations of the LJ EOS from LJ simulation data.

PHAHST Potential: Modeling Sorption in a Dispersion-Dominated Environment.

PHAHST (potentials with high accuracy, high speed, and transferability) is a recently developed force field that utilizes exponential repulsion, multiple dispersion terms, explicit many-body polarization, and many-body van der Waals interactions. The result is a systematic approach to force field development that is computationally practical. Here, PHAHST is employed in the simulation for rare gas uptake of krypton and xenon in the metal-organic material, HKUST-1. This material has shown promise in use as an adsorptive separating agent and presents a challenge to model due to the presence of heterogeneous interaction sorption surfaces, which include pores with readily accessible, open-metal sites that compete with dispersion-dominated pores. Such environments are difficult to simulate with commonly used empirical force fields, such as the Lennard-Jones (LJ) potential, which perform better when electrostatics are dominant in determining the nature of sorption and alone are incapable of modeling interactions with open-metal sites. The effectiveness of PHAHST is compared to the LJ potential in a series of mixed Kr-Xe gas simulations. It has been demonstrated that PHAHST compares favorably with experimental results, and the LJ potential is inadequate. Overall, we establish that force fields with physically grounded repulsion/dispersion terms are required in order to accurately model sorption, as these interactions are an important component of the energy. Furthermore, it is shown that the simple mixing rules work nearly quantitatively for the true pair potentials, while they are not transferable for effective potentials like LJ.

Engineered nanoparticles as Selinexor drug delivery systems across the cell membrane and related signaling pathways in cancer cells

In the present work, molecular dynamics simulation is applied to evaluate the drug carrier efficiency of graphene oxide nanoflake (GONF) for loading of Selinexor (SXR) drug as well as the drug delivery by 2D material through the membrane in aqueous solution. In addition, to investigate the adsorption and penetration of drug-nanocarrier complex into the cell membrane, well-tempered metadynamics simulations and steered molecular dynamics (SMD) simulations were performed. Based on the obtained results, it is evident that intermolecular hydrogen bonds (HBs) and π-π interactions play a significant role in expediting the interaction between drug molecules and the graphene oxide (GO) nanosheet, ultimately resulting in the formation of a stable SXR-GO complex. The Lennard-Jones (L-J) energy value for the interaction of SXR with GONF is calculated to be approximately −98.85 kJ/mol. In the SXR-GONF complex system, the dominant interaction between SXR and GONF is attributed to the L-J term, resulting from the formation of a strong π−π interaction between the drug molecules and the substrate surface. Moreover, our simulations show by decreasing the distance of GONF with respect to cell membrane, the interaction energy of GONF-membrane significantly decrease to −1500 kJ/mol resulting in fast diffusion of SXR-GONF complex toward the bilayer surface that is favored opening the way to natural drug nanocapsule.

Performance of Particle Swarm Optimization in Predicting the Orientation of π-Conjugated Molecules Inside Carbon Nanotubes Compared with Density Functional Theory Calculations.

Particle swarm optimization (PSO) was employed to obtain the global minimum of host-guest structures consisting of a triiodobenzene molecule (BzI3) inside an armchair (m,m) nanotube (BzI3@(m,m)), whose host-guest interactions are approximated by Lennard-Jones (LJ) potentials. The host-guest structures obtained using the PSO-LJ method were then compared with those obtained through dispersion-corrected density functional theory (DFT) calculations to evaluate the performance of the PSO-LJ approach in predicting the guest orientation inside a tube. When the inner space of the host tube is limited for guest encapsulation, the PSO-LJ method can reproduce the DFT results of BzI3@(m,m) in terms of the guest orientation. Conversely, in nanotubes with a sufficiently large space to allow a guest to freely move, corresponding to weak tube confinement, the PSO-LJ method yields guest orientations that are different from those obtained through DFT calculations; however, both methods obtain energetically close guest orientations. Accordingly, PSO-LJ method-assisted DFT calculations can quickly provide energetically stable guest orientations in BzI3@(m,m) in weak tube confinement, which can be ignored in DFT calculations, where a single initial geometry is typically used.

Exploring surface properties and premelting in crystals.

Crystal surfaces play a pivotal role in governing various significant processes, such as adsorption, nucleation, wetting, friction, and wear. A fundamental property that influences these processes is the surface free energy, γ. We have directly calculated γ(T) for low-index faces of Lennard-Jones (LJ), germanium, and silicon crystals along their sublimation lines using the computational cleavage technique. Our calculations agree well with experimental values for Si(111) and Ge(111), highlighting the accuracy of the method and models used. For LJ crystals, we identified a premelting onset at Tpm = 0.75Tm, marked by a sharp increase in atom mobility within the second outermost surface layer. Notably, Tpm closely aligned with the endpoint of the LJ melting line at negative pressures, Tend = 0.76Tm. We hypothesize that the emergence and coexistence of a liquid film atop the LJ crystal at Tpm < T < Tm correspond to the metastable melting line under negative pressures experienced by stretched crystal surfaces. Furthermore, our study of thin LJ crystal slabs reveals that premelting-induced failure leads to recrystallization below the homogeneous freezing limit, offering a promising avenue to explore crystal nucleation and growth at extremely deep supercoolings. Finally, no evidence of premelting was detected in the model crystals of Ge and Si, which is consistent with the experimental observations. Overall, our findings offer valuable insights into crystal surface phenomena at the atomic scale.

A Simple Generic Model of Elastin-Like Polypeptides with Proline Isomerization.

A generic model of elastin-like polypeptides (ELP) is derived that includes proline isomerization (ProI). As a case study, conformational transition of a -[valine-proline-glycine-valine-glycine]- sequence is investigated in aqueous ethanol mixtures. While the non-bonded interactions are based on the Lennard-Jones (LJ) parameters, the effect of ProI is incorporated by tuning the intramolecular 3- and 4-body interactions known from the underlying all-atom simulations into the generic model. One of the key advantages of such a minimalistic model is that it readily decouples the effects of geometry and the monomer-solvent interactions due to the presence of ProI, thus gives a clearer microscopic picture that is otherwise rather nontrivial within the all-atom setups. These results are consistent with the available all-atom and experimental data. The model derived here may pave the way to investigate large scale self-assembly of ELPs or biomimetic polymers ingeneral.

Study of the thermodynamic inconsistency of the potential of mean force calculated using the integral equation theory of molecular liquids

In this study, we investigated thermodynamic inconsistency in the potential of mean force (PMF) calculated using the Ornstein-Zernike (OZ), one-dimensional reference interaction site model (1D-RISM), and three-dimensional OZ (3D-OZ) theories. Two methods were used to obtain the PMF: converting the radial distribution function (RDF) into the PMF, and utilizing the solvation free energy (SFE) of the diatomic solute molecule with an added direct interaction between the two solute atoms. Both for the Lennard-Jones (LJ) and Coulomb systems, the hypernetted chain (HNC) closure showed the best performance among the closure relationships tested in this study. However, the performance of the HNC was not perfect and exhibited significant inconsistency in the PMF. The Kovalenko–Hirata and Kobryn–Gusarov–Kovalenko closures were also tested, with fair results when combined with the 1D-RISM equation but poor results when combined with the 3D-OZ equation. The Verlet-modified (VM) closure was found to be inapplicable to Coulomb systems. In contrast, the modified HNC (MHNC) closure showed relatively good results at high temperatures. Furthermore, we modified the Martynov–Sarkisov (MS) closure for Coulomb systems, resulting in a modified MS closure that yields relatively accurate PMF results. We also discuss the behavior of the SFE for Coulomb systems obtained from the 1D-RISM theory, a thorough analysis of both the RDF and the integrand in the Kirkwood charging formula.

An Efficient Growth Pattern Algorithm (GrowPAL) for Cluster Structure Prediction.

Identifying the lowest energy isomers in large clusters is a major challenge. Here, we introduce the Growth Pattern Algorithm (GrowPAL), a new approach that generates initial seeds composed of n+1 atoms from the system with n atoms through an interstitial-type addition (I-type) mechanism. We evaluated the effectiveness of GrowPAL on Lennard-Jones (LJ) clusters with up to n = 80 atoms, verifying the algorithm's ability to find challenging minima such as LJ38 and the partially icosahedral LJ69 with fewer optimizations than existing methods. In addition, we discuss the advantages and limitations of GrowPAL using our deconstruction scheme, which identifies "forebears" structures to study growth pathways. Having evaluated the strengths and weaknesses of GrowPAL, we employed it to explore Sutton-Chen clusters containing 5 to 80 atoms, uncovering three new lowest energy forms. We then applied GrowPAL to boron clusters containing 8 to 15 atoms, successfully identifying all reported minima. Overall, GrowPAL offers a practical solution for efficiently identifying global minima in hierarchical systems, thereby reducing computational costs.

On the History of the Lennard‐Jones Potential

AbstractThis contribution describes two episodes from the history of the Lennard‐Jones (LJ) potential. The first, located in the 1920s and 1930s, is about a computational approach that aimed at pragmatics rather than truth and that remained remarkably robust when quantum theory arrived. The second episode covers the birth of the LJ substance in 1964. Due to increasing interest in computer methods, simulated model substances became objects on their own, the prime targets of investigation. The history of the LJ potential and substance exemplifies the dynamic relationship between prediction, theory, mathematization, and computer instrumentation.

Binding of Phosphate Species to Ca2+ and Mg2+ in Aqueous Solution.

Phosphate derivatives and their interaction with metal cations are involved in many important biological phenomena, so an accurate characterization of the phosphate-metal interaction is necessary to properly understand the role of phosphate-metal contacts in mediating biological function. Herein, we improved the standard 12-6 Lennard-Jones (LJ) potential via the usage of the 12-6-4 LJ model, which incorporates ion-induced dipole interactions. Via parameter scanning, we fine-tuned the 12-6-4 LJ polarizability values to obtain accurate absolute binding free energies for the phosphate anions H2PO4-, HPO42-, PO43- coordinating with Ca2+ and Mg2+. First, we modified the phosphate 12-6-4 LJ parameters to reproduce the solvation free energies of the series of phosphate anions using the thermodynamic integration (TI) method. Then, using the potential mean force (PMF) method, the polarizability of the metal-phosphate interaction was obtained. We show that the free energy profiles of phosphate ions coordinated to Ca2+ and Mg2+ generally show similar trends at longer metal-phosphate distances, while the absolute binding energy values increased with deprotonation. The resulting parameters demonstrate the flexibility of the 12-6-4 LJ-type nonbonded model and its usefulness in accurately describing cation-anion interactions.

Ionic hydration at ambient and higher pressures: Computed chemical potentials from simulations and finite-size effects

For the chemical potential of a hydrated mono-atomic ion, finite- size effects on simulation results obtained using molecular potential truncation are investigated. Free energy perturbation (FEP) calculations were carried out by scaling in two processes the Lennard-Jones (LJ) ion-water parameters and the ion-charge (q) for Br−, K+ and Ca2+ interacting with TIP4P water. Corrections which scale with q2 enable us to reduce finite-size effects. However, at ambient conditions, discrepancies which depend on q are shown by the corrected values when comparison is made with the experimental data of the Marcus compilation. Similar behavior was observed by extrapolating the original FEP results to an infinitely large system. Hence, these errors were assumed to depend on water density and corrected at high pressures. Consistency, within statistical uncertainties, is shown when comparing with results derived from computed volumetric quantities. Results are also compared with those derived from experimental values of excess volumes at ambient conditions.

Coarse-grained molecular dynamics model of AB diblock copolymers composed of blocks with different Lennard-Jones parameters forming lamellar structures

In thermoplastic elastomers, the structure formation of hard and soft domains and the mechanical response to deformation remain vital areas of interest. To realize the coarse-grained molecular dynamics (CGMD) simulations of systems incorporating the difference in glass transition temperature Tg between domains, we studied AB diblock copolymers (di-BCPs) with asymmetric Lennard-Jones (LJ) parameters (the strength coefficient εLJ and cutoff length rc). For instance, hard and soft domains were realized by assigning the cutoff lengths of each segment to rc,(A,A) = 2.5 (high Tg) and rc,(B,B) = 1.5 (low Tg), respectively. To identify how the cutoff length rc,(B,B) corresponds to the strength coefficient ε(B,B) in the phase separation behavior against the fixed LJ parameters for the A block (rc,(A,A) = 2.5 and ε(A,A) = 1.0), we focused on lamellar structures in which the A and B blocks possess equal segment numbers. For the asymmetric cases with rc,(B,B) < rc,(A,A), we estimated the effective ε(B,B)' on the basis of the DA/DB ratio of the partial domain spacings. We confirmed that the scaling relations (D ∼ Δε1/6, D/N0.7 ∼ Δε, and D/N1/2 ∼ ΔεN) hold, where ε(A,A) = 1, Δε = ((1 + ε(B,B)')/2 – ε(A,B)), and N denotes the number of segments per AB di-BCP chain. Therefore, this work will provide valuable insights for guiding applied research on BCPs.

FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation.

Developing production quality CHARMM force-field (FF) parameters is a very detailed process involving a variety of calculations, many of which are specific for the molecule of interest. The first version of FFParam was developed as a standalone Python package designed for the optimization of electrostatic and bonded parameters of the CHARMM additive and polarizable Drude FFs by using quantum mechanical (QM) target data. The new version of FFParam has multiple new capabilities for FF parameter optimization and validation, with an emphasis on the ability to use condensed-phase target data in optimization. FFParam-v2 allows optimization of Lennard-Jones (LJ) parameters using potential energy scans of interactions between selected atoms in a molecule and noble gases, viz., He and Ne, and through condensed-phase calculations, from which experimental observables such as heats of vaporization and free energies of solvation may be obtained. This functionality serves as a gold standard for both optimizing parameters and validating the performance of the final parameters. A new bonded parameter optimization algorithm has been introduced to account for simultaneously optimizing multiple molecules sharing parameters. FFParam-v2 also supports the comparison of normal modes and the potential energy distribution of internal coordinates towards each normal mode obtained from QM and molecular mechanics calculations. Such comparison capability is vital to validate the balance among various bonded parameters that contribute to the complex normal modes of molecules. User interaction has been extended beyond the original graphical user interface to include command-line interface capabilities that allow for integration of FFParam in workflows, thereby facilitating the automation of parameter optimization. With these new functionalities, FFParam is a more comprehensive parameter optimization tool for both beginners and advanced users.

Theoretical prediction and regulation of interlayer stable angle in twisting bilayer graphene

Recent researches showed that interlayer rotation, as a control method, can effectively regulate the mechanical, electrical, and optical properties of two-dimensional (2D) materials. The control of the twisting angle and its stability influence the properties of rotation-tunable electronics, so it has attracted much attention. In this research, based on the Lennard-Jones (L-J) potential and energy density method, the energy landscape of twisted bilayer graphene (tBLG) is studied. The dependence of the locally stable twisting angle and the number of potential energy barriers on the size of the top layer graphene is analyzed. It is found that the size effect is related to the vertical distance between carbon atoms and the rotation axis. The large-sized top layer graphene has a larger energy barrier and higher stability under the same conditions, which is conducive to the structural stability of the rotation-tunable electronics. The vacancy defect and the shape of the top layer graphene have an effect on the energy landscape, based on which the regulation of stable twisting angle can be achieved. In addition, the effect of the position of the top layer graphene on the energy landscape is studied, and it is found that the energy landscape has a 2D periodicity with the change of the position, which is related to the lattice structure of graphene. There are two main modes of energy landscape with the variation of the position of top layer graphene, and the changing trend is similar under the same mode. Our research predicts the interlayer stable twisting angle theoretically and provides theoretical support for the design of rotation-tunable electronics.

Homogeneous crystallization in four-dimensional Lennard-Jones liquids.

We observe homogeneous crystallization in simulated high-dimensional (d>3) liquids that follow physically realistic dynamics and have system sizes that are large enough to eliminate the possibility that crystallization was induced by the periodic boundary conditions. Supercooled four-dimensional (4D) Lennard-Jones (LJ) liquids maintained at zero pressure and constant temperatures 0.59<T<0.63 crystallized within ∼2×10^{4}τ, where τ is the LJ time unit. Weeks-Chandler-Andersen (WCA) liquids that were maintained at the same densities and temperatures at which their LJ counterparts nucleated did not crystallize even after 2.5×10^{5}τ, showing that the presence of long-ranged attractive interactions dramatically speeds up 4D crystallization, much as it does in 3D. On the other hand, the overlap of the liquid and crystalline phases' local-bond-order distributions is smaller for LJ systems than for WCA systems, which is the opposite of the 3D trend. This implies that the widely accepted hypothesis that increasing geometrical frustration rapidly suppresses crystallization as the spatial dimension d increases is only generally valid in the absence of attractive interparticle forces.

Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field.

Molecular dynamics (MD) simulations are a commonly used method for investigating molecular behavior at the atomic level. Achieving reliable MD simulation results necessitates the use of an accurate force field. In the present work, we present a protocol to enhance the quality of group 1 monatomic ions (specifically Li+, Na+, K+, Rb+, and Cs+) with respect to their interactions with common polar model compounds in biomolecules in condensed phases in the context of the Drude polarizable force field. Instead of adjusting preexisting individual parameters for ions, model compounds, and water, we employ atom-pair specific Lennard-Jones (LJ) (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) terms to fine-tune the balance of ion-model compound, ion-water, and model compound-water interactions. This involved establishing a protocol for the optimization of NBFIX and NBTHOLE parameters targeting the difference between molecular mechanical (MM) and quantum mechanical (QM) potential energy scans (PES). It is shown that targeting PES involving complexes that include multiple model compounds and/or ions as trimers and tetramers yields parameters that produce condensed phase properties in agreement with experimental data. Validation of this protocol involved the reproduction of experimental thermodynamic benchmarks, including solvation free energies of ions in methanol and N-methylacetamide, osmotic pressures, ionic conductivities, and diffusion coefficients within the condensed phase. These results show the importance of including more complex ion-model compound complexes beyond dimers in the QM target data to account for many-body effects during parameter fitting. The presented parameters represent a significant refinement of the Drude polarizable force field, which will lead to improved accuracy for modeling ion-biomolecular interactions.

Evaluation and improvement of Gay-Berne interaction potential to simulate 3D DLVO interaction of clay particles

This paper first presents a set of DLVO-based energy-separation functions for a pair of finite uniformly charged square platelets of infinitesimal thickness in three elementary configurations: face-to-face, edge-to-edge, and edge-to-face. The novel dataset was generated by summing the electrostatic interaction energy computed numerically by solving the non-linear 3D Poisson-Boltzmann equation and the van der Waals interaction energy calculated analytically. The dataset aims to inform qualitatively and quantitatively the energy/force separation functions used in the Discrete Element Method (DEM) and Coarse-Grained Molecular Dynamics (CGMD) modelling of clays. The same dataset was then used to calibrate and evaluate two Gay-Berne (GB)-type potentials: i) a DLVO-adapted Gay-Berne potential, where the Born-van der Waals branches of the underlying Lennard-Jones (LJ) potential are replaced with van der Waals-Columbic branches to represent DLVO interactions; ii) the Mie potential, where the exponents of the two energy terms are ‘unlocked’ instead of being set equal to 12 and 6 as per the original LJ potential. It is shown that the orientation parameter, µ, and the anisotropy parameter, ν, need to be different from µ = 2 and ν = 1 as adopted in CGMD clay modelling to capture the progression of the shape of the pair energy-separation function from face-to-face to edge-to-face and edge-to-edge configuration. It is also shown that the MIE potential (with exponents m = 3 and n = 1.5) better captures the slow decay of the electrostatic repulsive energy component of the DLVO potential energy Coulombic branch of the interaction potential compared to the DLVO-adapted GB potential, which embeds the Lennard-Jones (LJ) exponents m = 12 and n = 6.

A molecular dynamics simulation study of thermal transport in hydrazinium cyclo-pentazolate

Cyclo-pentazolate salts (CPSs) as a new type of high-energy-density materials (HEDMs) with high nitrogen content have attracted considerable research attention. In contrast to the extensive studies on their energy properties, the thermal transport process in CPSs has been less studied which relates closely to the thermal safety of this material. Concerning the hydrazinium cyclo-pentazolate (HCP), we conduct a computational study to estimate the thermal conductivity of HCP by means of the non-equilibrium molecular dynamics (NEMD) simulation. To achieve that, we have customized interaction parameters based on the default OPLS force field for the HCP, as benchmarked by its crystal structure. Our simulations have revealed surprisingly anisotropic thermal conductivity for the HCP, while the thermal conductivity becomes highest roughly in the direction perpendicular to cyclo-N 5− with its value notably higher than common high explosives. By modulating the interaction parameters within the HCP molecule, we have further captured a dominant role of the interaction between cyclo-N 5− in regulating the thermal conductivity of the HCP. The attractive Lennard–Jones (LJ) potential may restrict the relative motion between cyclo-N 5− , which forms a long-range order thus enhances thermal transport in the direction perpendicular to cyclo-N 5− . Our simulations result on the effect of (cyclo-N 5− )-(cyclo-N 5− ) interaction provide insights to engineer thermal transport in CPSs at the molecular level.

Tracer dynamics in polymer networks: Generalized Langevin description.

Tracer diffusion in polymer networks and hydrogels is relevant in biology and technology, while it also constitutes an interesting model process for the dynamics of molecules in fluctuating, heterogeneous soft matter. Here, we systematically study the time-dependent dynamics and (non-Markovian) memory effects of tracers in polymer networks based on (Markovian) implicit-solvent Langevin simulations. In particular, we consider spherical tracer solutes at high dilution in regular, tetrafunctional bead-spring polymer networks and control the tracer-network Lennard-Jones (LJ) interactions and the polymer density. Based on the analysis of the memory (friction) kernels, we recover the expected long-time transport coefficients and demonstrate how the short-time tracer dynamics, polymer fluctuations, and the viscoelastic response are interlinked. Furthermore, we fit the characteristic memory modes of the tracers with damped harmonic oscillations and identify LJ contributions, bond vibrations, and slow network relaxations. Tuned by the LJ interaction parameter, these modes enter the kernel with an approximately linear to quadratic scaling, which we incorporate into a reduced functional form for convenient tracer memory interpolation and extrapolation. This eventually leads to highly efficient simulations utilizing the generalized Langevin equation, in which the polymer network acts as an additional thermal bath with a tunable intensity.