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Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica: dataset

Abstract: (from [1]) <blockquote> The addition of fillers can significantly improve the mechanical behavior of polymers. The responsible mechanisms at the molecular level can be well assessed by particle-based simulation techniques, such as molecular dynamics. However, the high computational cost of these simulations prevents the study of macroscopic samples. Continuum-based approaches, particularly micromechanics, offer a more efficient alternative but require precise constitutive models for all constituents, which are usually unavailable at these small length scales. In this contribution, we derive a molecular-dynamics-informed constitutive law by employing a characterization strategy introduced in a previous publication. We choose silicon dioxide (silica) as an exemplary filler material used in polymer composites and perform uniaxial and shear deformation tests with molecular dynamics. The material exhibits elastoplastic behavior with a pronounced anisotropy. Based on the pseudo-experimental data, we calibrate an anisotropic elastic constitutive law and reproduce the material response for small strains accurately.   The study validates the characterization strategy that facilitates the calibration of constitutive laws from molecular dynamics simulations. Furthermore, the obtained material model for coarse-grained silica forms the basis for future continuum-based investigations of polymer nanocomposites. In general, the presented transition from a fine-scale particle model to a coarse and  computationally efficient continuum description adds to the body of knowledge of molecular science as well as the engineering community.   </blockquote> Contact: Maximilian Ries Institute of Applied Mechanics Friedrich-Alexander-Universität Erlangen-Nürnberg Egerlandstr. 5 91058 Erlangen Software: All simulations were performed with LAMMPS [3], version: 29 Oct 2020 / 20201029 Compiled with Compiler: GNU C++ 4.8.5 20150623 (Red Hat 4.8.5-39) with OpenMP not enabled C++ standard: C++11 Active compile time flags: -DLAMMPS_GZIP -DLAMMPS_SMALLBIG Installed packages: CLASS2, KSPACE, MANYBODY, MC, MOLECULE, MPIIO, OPT, VORONOI, USER-INTEL, USER-MISC, USER-MOLFILE, USER-NETCD License: Creative Commons Attribution 4.0 International   Context: Data set supplementing  journal paper: [1] Ries, M.; Bauer, C.; Weber, F.; Steinmann, P. & Pfaller, S., "Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica", Mathematics and Mechanics of Solids, 2022, 108128652211080. This dataset contains the results presented in [1] and the necessary data to obtain those. Content: The files to reproduce our simulations and their results are structured as follows: <ul> <li>01_potentials tabulated potentials calibrated via iterative Boltzmann inversion in [2] kindly provided by the Müller-Plathe group at Technische Universität Darmstadt <ul> <li>Angle_table angular interactions</li> <li>Bond_table bond interactions</li> <li>Nonbond_table pair interactions</li> </ul> </li> <li>02_sample Lammps data file (molecular style) of the investigated silica sample</li> <li>03_simulations The condensed simulation directories with the naming convention given below are organized in the following subfolders: <ul> <li>01_time-proportional time-proportional simulation data</li> <li>02_time-periodic time-periodic simulation data</li> </ul> </li> </ul> Each simulation directory contains: <ul> <li>lammps input file (*.in) of the specific simulation</li> <li>input.prm: input parameters of the specific simulation (read by the input file)</li> <li>meta.info: meta data of the specific simulation run</li> <li>LAMMPS_out: simulation results (lammps thermo_out) in tabulated form, an overview of columns is given below <ul> <li>thermo_out.Dat: raw output</li> <li>thermo_out_SG.Dat: smoothed output (Savitzky-Golay filter)</li> <li>thermo_out_STD.Dat: standard deviation of raw output</li> </ul> </li> </ul> Naming convention: Silica-[deformation]-[direction]_[deformation function]-[deformation magnitude]_[deformation rate] ●    [deformation]: uniaxial tension (UT), simple shear (SS) ●    [direction]: deformation carried out in X/Y/Z (UT) or XY/XZ/YZ (SS) ●    [deformation function]: time-proportional (strain), time-periodic (strain_ampl) ●    [deformation magnitude]: maximum strain (time-proportional), strain amplitude (time-periodic); unitless ●    [deformation rate]: rate-[strain rate] (only time-proportional): 0.001/ns-0.1/ns Output quantities (columns of *.Dat files): ●    Step: time step ●    Time: time in fs ●    TotEng: total energy in kcal/mol ●    PotEng: potential energy in kcal/mol ●    KinEng: kinetic energy in kcal/mol ●    E_pair: pair energy in kcal/mol ●    E_bond: bond energy in kcal/mol ●    E_angle: angle energy in kcal/mol ●    E_dihed: dihedral energy in kcal/mol ●    Temp: temperature in K ●    Press: hydrostatic pressure in atm ●    Pxx: xx component of pressure tensor in atm ●    Pyy: yy component of pressure tensor in atm ●    Pzz: zz component of pressure tensor in atm ●    Pxy: xy component of pressure tensor in atm ●    Pxz: xz component of pressure tensor in atm ●    Pyz: yz component of pressure tensor in atm ●    Volume: volume of simulation box in (Angstroms)^3 ●    Lx: box length in x direction in Angstroms ●    Ly: box length in y direction in Angstroms ●    Lz: box length in z direction in Angstroms ●    Density: density in g/(cm^3) ●    c_RG: radius of gyration in Angstroms ●    c_RG[1]: squared radius of gyration tensor (xx component) in (Angstroms)^2 ●    c_RG[2]: squared radius of gyration tensor (yy component) in (Angstroms)^2 ●    c_RG[3]: squared radius of gyration tensor (zz component) in (Angstroms)^2 ●    c_RG[4]: squared radius of gyration tensor (xy component) in (Angstroms)^2 ●    c_RG[5]: squared radius of gyration tensor (xz component) in (Angstroms)^2 ●    c_RG[6]: squared radius of gyration tensor (yz component) in (Angstroms)^2 ●    c_bondave[1]: bond energy averaged over all atoms in kcal/mol ●    c_bondave[2]: bond distance averaged over all atoms in  Angstroms ●    c_bondave[3]: squared bond distance averaged over all atoms in (Angstroms)^2 ●    c_angleave[1]: angle energy averaged over all atoms in kcal/mol ●    c_angleave[2]: angle averaged over all atoms degree ●    c_angleave[3]: cosine of angle (unitless) ●    c_angleave[4]: squared cosine of angle (unitless) ●    c_MSD[1]: mean squared displacement x-direction in (Angstroms)^2 ●    c_MSD[2]: mean squared displacement y-direction in (Angstroms)^2 ●    c_MSD[3]: mean squared displacement z-direction in (Angstroms)^2 ●    c_MSD[4]: total mean squared displacement in (Angstroms)^2 ●    c_COM[1]: x coordinate of center of mass in Angstroms ●    c_COM[2]: y coordinate of center of mass in Angstroms ●    c_COM[3]: z coordinate of center of mass in Angstroms ●    v_strain_xx: xx component of engineering strain tensor (unitless)   ●    v_strain_yy: yy component of engineering strain tensor (unitless)    ●    v_strain_zz: zz component of engineering strain tensor (unitless)    ●    v_vMisesequivstress: von Mises equivalent stress in MPa ●    v_Cauchy_xx: xx component of stress tensor in MPa   ●    v_Cauchy_yy: yy component of stress tensor in MPa ●    v_Cauchy_zz: zz component of stress tensor in MPa ●    v_Cauchy_xy: xy component of stress tensor in MPa ●    v_Cauchy_xz: xz component of stress tensor in MPa ●    v_Cauchy_yz: yz component of stress tensor in MPa ●    v_strain_xy: xy component of engineering strain tensor (unitless)   ●    v_strain_xz: xz component of engineering strain tensor (unitless)   ●    v_strain_yz: yz component of engineering strain tensor (unitless)   References: [1] Ries, M.; Bauer, C.; Weber, F.; Steinmann, P. & Pfaller, S., "Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica", Mathematics and Mechanics of Solids, 2022, 108128652211080. [2] Ghanbari, A.; Ndoro, T. V. M.; Leroy, F.; Rahimi, M.; Böhm, M. C. & Müller-Plathe, F., “Interphase Structure in Silica-Polystyrene Nanocomposites: A Coarse-Grained Molecular Dynamics Study”, Macromolecules, 2012, 45, 572-584. [3] Plimpton, S., “Fast parallel algorithms for short-range molecular dynamics,” Journal of computational physics, 1995, 117, 1-19.

Figure 4 in The parasitism of Persian jird by immature stages of Hyalomma asiaticum (Acari: Ixodidae) and its identification using molecular approaches in Iran

Figure 4. One percent agarose gel electrophoresis stained with Cyber Safe® showing 5.8S/ITS2 gene fragments amplified using Fanas/Ras for H. asiaticum with amplicon size 408 bp (100 bp DNA ladder). Numbers below bands representing location of collected specimens according to Fig. 4.

Figure 3 in The parasitism of Persian jird by immature stages of Hyalomma asiaticum (Acari: Ixodidae) and its identification using molecular approaches in Iran

Figure 3. Immatures of Hyalomma asiaticum collected from Meriones persicus in western Iran (nymphal stage): left: dorsal and right: ventral views.

Figure 5 in The parasitism of Persian jird by immature stages of Hyalomma asiaticum (Acari: Ixodidae) and its identification using molecular approaches in Iran

Figure 5. Phylogenetic tree of Hyalomma asiaticum ticks inferred from ITS2 sequence data constructed using Bayesian Inference (BI) method. Nodes indicated with posterior probability values. Branch lengths are proportional to evolutionary changes (substitutions/site). Tree was rooted by Rhipicephalus sanguineus.

Figure 1 in The parasitism of Persian jird by immature stages of Hyalomma asiaticum (Acari: Ixodidae) and its identification using molecular approaches in Iran

Figure 1. Three rodent collection sites located in Lorestan province western Iran inlcuding: 1. Khorramabad-Kuhdasht road, Zamzam village; 2. Khorramabad-Tehran road, LUMS Campus; 3. Dorud-Azna road, Zarnan village.

Figure 2. A in The parasitism of Persian jird by immature stages of Hyalomma asiaticum (Acari: Ixodidae) and its identification using molecular approaches in Iran

Figure 2. A rodent specimen infested by a number of immature ticks (red arrow) (animal is restrained through the ear by forceps and treated by insecticied for killing of ectoparasites).

Fig. 5 in A new blood parasite of leaf warblers: molecular characterization, phylogenetic relationships, description and identification of vectors

Fig. 5 Sporogonic stages of Haemoproteus homopalloris n. sp. in tce biting midge Culicoides nubeculosus. Zygote (a) and sporozoite (b). Arrowcead: pigment granuges; arrow: sporozoite nucgeus. Metcanog-fixed and Giemsa-stained tcin figms. Scale-bar: a, b, 10 μm

Fig. 2 in A new blood parasite of leaf warblers: molecular characterization, phylogenetic relationships, description and identification of vectors

Fig. 2 Bayesian pcygogenetic inference of cytb gene gineages (479 bp) of 35 Haemoproteus spp. Tce tree is rooted witc Leucocytozoon sp. (gineage gSISKIN2). Cgades A and B indicate species of tce subgenus Parahaemoproteus (a) and caemoproteids witc page-staining cytopgasm of gametocytes (b). MagAvi gineage codes are provided, foggowed by parasite species names and GenBank accession numbers. Nodag support vagues indicate Bayesian posterior probabigities. New species is given in bogd

Fig. 1 in A new blood parasite of leaf warblers: molecular characterization, phylogenetic relationships, description and identification of vectors

Fig. 1 Gametocytes of two species of caemoproteids described from geaf warbges, Pcyggoscopidae. Haemoproteus homopalloris n. sp. (a-l) and Haemoproteus palloris (m-p). Young gametocytes (a, b), macrogametocytes (c-g, m, n) and microgametocytes (h-l, o, p). Long arrows: gametocyte nucgei; scort arrows: vacuoge-gike spaces in macrogametocytes; arrowceads: pigment granuges. Giemsa-stained tcin bgood figms. Scale-bar: a-p, 10 μm

Fig. 4 in A new blood parasite of leaf warblers: molecular characterization, phylogenetic relationships, description and identification of vectors

Fig. 4 Gametocytes of two species of caemoproteids, wcicc cave been reported in tce wood warbger Phylloscopus sibilatrix. Macrogametocytes (a-c, e-g) and microgametocytes (d, h) of Haemoproteus majoris (a-d) and H. belopolskyi (e-h). Note tcat tce intensity of staining of tce cytopgasm is different in macro- and microgametocytes. Long arrows: gametocyte nucgei; scort arrows: vacuoge-gike spaces in macrogametocytes; arrowceads: pigment granuges. Giemsa-stained tcin bgood figms. Scale-bar: a-h, 10 μm

Fig. 3 in A new blood parasite of leaf warblers: molecular characterization, phylogenetic relationships, description and identification of vectors

Fig. 3 Haemoproteus spp. witc page staining of macrogametocyte cytopgasm. Haemoproteus concavocentralis (a-d), H. minutus (e-h), H. pallidus (i- l), H. pallidulus (m-p) and H. vacuolatus (q-t). Macrogametocytes (a, b, e, f, i, j, m, n, q, r), microgametocytes (c, d, g, h, k, l, o, p, s, t). Note tce foggowing vaguabge diagnostic features of tce parasites: presence of a space between tce nucgeus of tce infected erytcrocyte and tce growing gametocyte in H. concavocentralis (a); cgeargy irregugar outgine of mature gametocytes, wcicc do not toucc tce poges of infected erytcrocytes in H. minutus (e-h); gametocyte wcicc are cgosegy appressed to tce nucgeus of erytcrocyte but do not toucc tce envegope of erytcrocyte agong tceir entire margin in H. pallidus (j, l); smagg pigment granuges in mature gametocytes of H. pallidulus (m-p); presence of one prominent vacuoge in tce cytopgasm of eacc advanced macrogametocyte in H. vacuolatus (q-t). Agg tcese features are not ccaracteristics of H. homopalloris n. sp. (see Fig. 1). Long simpge arrows: gametocyte nucgei; scort simpge arrows: vacuoge-gike spaces in macrogametocytes; arrowceads: pigment granuges; gong simpge wide arrows: space present between tce parasite and an infected erytcrocyte nucgeus (a, d) and space between tce parasite and tce envegope of infected erytcrocyte (j, l). Giemsa-stained tcin bgood figms. Scale-bar: a-t, 10 μm

Fig. 6 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 6 Maximum likelihood (ML) phylogram reconstructed using the 18S rDNA dataset of the new species Huffmanela persica sp. nov. and other related species within the families Trichosomoididae,Trichinellidae, Trichuridae and Capillariidae. ML analysis was performed using the substitution model K2 + G with 1000 bootstrap replications

Fig. 5 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 5 Photomicrographs from histological sections of infected tissues of a daggertooth pike conger eel. A, B Histological sections of the stomach infected by eggs of Huffmanela persica sp. nov. at various stages of development as well as degenerated encysted metazoans (⁎). C, D Sections of the tunica serosa of the stomach parasitized with completely developed eggs. E Sections of the ovarian lamellae infected by both clusters of immature (➔) and developing (➤) eggs, representing immature and previtellogenic oocytes embedded within a loose fibro-granulomatous infiltration containing histiocytes and eosinophilic granular leukocytes (⁎). F Magnified view of histological section of infected ovary showing a fibro-granulomatous infiltrate surrounding clusters of eggs at different stages of development (mainly highly developed eggs, ➤). G High magnification (100×) view of a fully developed egg of H. persica (cross-sectional view) showing larva in-folded within the eggshell and a protruding polar plug at either end. H Less developed eggs with a nearly central nucleus (⁎) and thin eggshell layer and I fully developed eggs containing twisted larvae of H. persica cut on varying planes of section

Fig. 4 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 4 Scanning electron micrographs of poorly developed (A–D) and fully developed (E–I) eggs of Huffmanela persica sp. nov. (separated from infected ovary). Less developed eggs spherical shaped (white arrow shows a shrunken and wrinkled egg) and with no evidently developed polar plugs. Fully developed eggs oblong and containing two plugs at poles. Eggs completely surrounded by a UL bearing uniformly based mammiform mounds adorned with tendril-like vermiform appendage emerging from the apex, occasionally adjoined to that of a neighboring mound (green arrowheads). Note the illusory appearance of serrated-like ridges (occasionally in the form of illusory interconnecting ridges, black arrows) in side views which is caused by overlapping of the mound bases (well observed in less developed eggs, red arrowheads). Outer surface of eggshell with irregular protuberances (yellow arrowheads)

Fig. 1 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 1 Representation of an advanced egg of Huffmanela persica sp. nov. with measurements considered in this study. Total length with protruding polar plug and UL (black line); total length without protruding polar plug and UL (red line); total width with UL (yellow line); total width without UL (light blue line); shell thickness with UL (green line); shell thickness without UL (white line); polar plug width (dark blue line)

Fig. 2 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 2 Macroscopic and microscopic appearance of fully developed eggs of Huffmanela persica sp. nov. A Grossly visible lesions of eggs previously deposited by adult forms of H. persica sp. nov. in the form of dark spots of various size within the infected tissues (ovary and serosa of stomach) of Muraenesox cinereus. B Wet mount prepared from infected ovary illustrating variously oriented advanced eggs of H. persica sp. nov. within the egg clusters

Fig. 3 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus

Fig. 3 General morphology and surface ornamentation pattern of eggs of Huffmanela persica sp. nov. in various stages of development. A–H Photomicrographs and a–h corresponding line drawings of individual eggs at different stages of development (scale bars: 20 µm). A, a Eggs in stage I at very early stage, probably meiosis I, with a spherical nucleus in granular cytoplasm and incompletely developed chitinous layer and polar plugs (note early appearance of superficial projections of UL already apparent). B, b Eggs in stage II at later stage of development (probably meiosis II); chitin deposition appears to be complete. C, c Two-celled mitotic stage of early embryonic development (embryonated). D, d Later multicellular stage of embryonic development; chitinous layer still uniformly translucent with no apparent division into outer and inner chitinous layers. E, e Eggs in stage III with bean-like embryo and chitinous layer appearing two-layered under bright-field (light) microscopy with darker inner layer. F, f Tadpole-like embryos with UL appearing to have been partially dislodged from chitinous layer. G, g Eggs in stage IV with darker-brown shell; embryo now vermiform (larvated) and in-folded three times (pretzel stage). H, h Later stage IV egg with chitinous layer very dark brown; larva nearing final development and folded 5–6 times. I–T Photomicrographs of less developed (I–L), moderately developed (M–P) and fully developed (Q–T) eggs, where the first set of images (I, M, Q) represents overview of these variously advanced eggs, and the second (J, N, R), third (K, O, S) and fourth (L, P, T) series of images focus on the pattern of their surface ornamentation by adjusting the focal plane. Black and yellow arrows represent illusions of superficial ridges (well demonstrated in less developed eggs; occasionally appearing as interconnecting ridges, blue arrowhead) and sculptures on the egg surface, respectively. Green arrowheads exhibit irregular protuberances on the eggshell surface. Red arrowheads indicate an illusory spinous appearance in fully developed eggs

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Fig. 4 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 4 Phylogenetic trees based on cox1 mtDNA (left tree) and ITS rDNA (right tree) sequences using the ML method with 1000 bootstraps

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Fig. 3 in Morphological and molecular identification of Cryptocotyle lingua metacercariae isolated from Atlantic cod (Gadus morhua) from Danish seas and whiting (Merlangius merlangus) from the English Channel

Fig. 3 Excysted Cryptocotyle lingua metacercariae at different degrees of contraction a in whiting from the English Channel, b in cod from Danish waters