This work was supported by the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program (grant agreement number 681818 IMPACT to RC), by the Extreme Physics and Chemistry Directorate of the Deep Carbon Observatory, and by the Research Council of Norway through its Centers of Excellence funding scheme, project number 223272. We acknowledge access to the GENCI supercomputers through the stl2816 series of eDARI computing grants, to the Irene AMD supercomputer through the PRACE RA4947 project, and the Fram supercomputer through the UNINETT Sigma2 NN9697K. FS was supported by a Marie Sk&#322;odowska-Curie project (grant agreement ABISSE No.750901).

<ol>
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P., Asimow, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+limitations+of+molecular+dynamic+simulations+as+probes+of+thermo-physical+behavior+of+silicate+melts.">Current limitations of molecular dynamic simulations as probes of thermo-physical behavior of silicate melts.</a> American Mineralogist. 100 (8-9), 1866-1882 (2015).</li><li>Caracas, R., Hirose, K., Nomura, R., Ballmer, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Melt-crystal+density+crossover+in+a+deep+magma+ocean.">Melt-crystal density crossover in a deep magma ocean.</a> Earth and Planetary Science Letters. 516, 202-211 (2019).</li><li>Green, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Markoff+Random+Processes+and+the+Statistical+Mechanics+of+Time-Dependent+Phenomena.+II.+Irreversible+Processes+in+Fluids.">Markoff Random Processes and the Statistical Mechanics of Time-Dependent Phenomena. II. Irreversible Processes in Fluids.</a> The Journal of Chemical Physics. 22 (3), 398-413 (1954).</li><li>Kubo, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical-Mechanical+Theory+of+Irreversible+Processes.+I.+General+Theory+and+Simple+Applications+to+Magnetic+and+Conduction+Problems.">Statistical-Mechanical Theory of Irreversible Processes. I. General Theory and Simple Applications to Magnetic and Conduction Problems.</a> Journal of the Physical Society of Japan. 12 (6), 570-586 (1957).</li><li>Lin, S. T., Blanco, M., Goddard, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+two-phase+model+for+calculating+thermodynamic+properties+of+liquids+from+molecular+dynamics:+Validation+for+the+phase+diagram+of+Lennard-Jones+fluids.">The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids.</a> The Journal of Chemical Physics. 119 (22), 11792-11805 (2003).</li><li>Meyer, E. R., Kress, J. D., Collins, L. A., Ticknor, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+correlation+on+viscosity+and+diffusion+in+molecular-dynamics+simulations.">Effect of correlation on viscosity and diffusion in molecular-dynamics simulations.</a> Physical Review E. 90 (4), 1198-1212 (2014).</li><li>Soubiran, F., Militzer, B., Driver, K. P., Zhang, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Properties+of+hydrogen,+helium,+and+silicon+dioxide+mixtures+in+giant+planet+interiors.">Properties of hydrogen, helium, and silicon dioxide mixtures in giant planet interiors.</a> Physics of Plasmas. 24 (4), 041401-041407 (2017).</li><li>Flyvbjerg, H., Petersen, H. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Error+estimates+on+averages+of+correlated+data.">Error estimates on averages of correlated data.</a> The Journal of Chemical Physics. 91 (1), 461-466 (1989).</li><li>Tuckerman, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Statistical mechanics: theory and molecular simulation. , (2010).</li><li>McDonough, W. F., Sun, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+composition+of+the+Earth.">The composition of the Earth.</a> Chemical Geology. 120, 223-253 (1995).</li><li>Elkins-Taton, L. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Magma+oceans+in+the+inner+solar+system.">Magma oceans in the inner solar system.</a> Annual Review of Earth and Planetary Sciences. 40, 113-139 (2012).</li><li>Lock, S. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+origin+of+the+Moon+within+a+terrestrial+synestia.">The origin of the Moon within a terrestrial synestia.</a> J. Geophysical Research: Planets. 123, 910-951 (2018).</li><li>Solomatova, N. 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The authors have nothing to disclose.

The UMD package has been designed to work better with ab initio simulations, where the number of snapshots is typically limited to tens to hundreds of thousands of snapshots, with a few hundred atoms per unit cell. Larger simulations are also tractable provided the machine on which the post-processing runs has enough active memory resources. The code distinguishes itself by the variety of properties it can compute and by its open-source license.
The umd.dat files are appropriate to the ensembles that preserve the number of particles unchanged throughout the simulation. The UMD package can read files stemming from calculations where the shape and volume of the simulation box varies. These cover the most common calculations, like NVT and NPT, where the number of particles, N, temperature T, volume, V, and/or pressure, P, are kept constant.
For the time begin the pair distribution function as well as all the scripts needing to estimate the interatomic distances, like the speciation scripts, work only for orthogonal unit cells, meaning for cubic, tetragonal, and orthorhombic cells, where the angles between the axes are 90&#176;.
The major lines of development for version 2.0 are removal of the orthogonality restriction for distances and adding more features for the speciation scripts: to analyze individual chemical bonds, to analyze the interatomic angles, and to implement the second coordination sphere. With help from external collaboration, we are working on porting the code onto a GPU for faster analysis in larger systems.

Fluids and melts are active chemical and physical transport vectors in natural environments. The elevated rates of atomic diffusion favor chemical exchanges and reactions, the low viscosity coupled with varying buoyancy favor large mass transfer, and crystal-melt density relations favor layering inside planetary bodies. The absence of a periodic lattice, typical high-temperatures required to reach the molten state, and the difficulty for quenching make the experimental determination of a series of obvious properties, like density, diffusion, and viscosity, extremely challenging. These difficulties make alternative computational methods strong and useful tools for investigating this class of materials.
With the advent of computing power and the availability of supercomputers, two major numerical atomistic simulations techniques are currently employed to study the dynamical state of a non-crystalline atomistic system, Monte Carlo1 and molecular dynamics (MD)1,2. In Monte Carlo simulations the configurational space is randomly sampled; Monte Carlo methods show linear scaling in parallelization if all sampling observations are independent of each other. The quality of the results depends on the quality of the random number generator and the representativeness of the sampling. Monte Carlo methods show linear scaling in parallelization if the sampling is independent of each other. In molecular dynamics (MD) the configurational space is sampled by time-dependent atomic trajectories. Starting from a given configuration, the atomic trajectories are computed by integrating the Newtonian equations of motion. The interatomic forces can be computed using model interatomic potentials (in classical MD) or using first-principles methods (in ab initio, or first-principles, MD). The quality of the results depends on the length of the trajectory and its capability to not be attracted to local minima.
Molecular dynamics simulations contain a plethora of information, all related to the dynamical behavior of the system. Thermodynamic average properties, like internal energy, temperature, and pressure, are rather standard to compute. They can be extracted from the output file(s) of the simulations and averaged, whereas quantities related directly to the movement of the atoms as well as to their mutual relation need to be computed after extraction of the atomic positions and velocities.
Consequently, a lot of effort has been dedicated to visualizing the results, and various packages are available today, on different platforms, open source or not [Ovito3, VMD4, Vesta5, Travis6, etc.]. All these visualization tools deal efficiently with interatomic distances, and as such, they allow the efficient computation of pair distribution functions and diffusion coefficients. Various groups performing large-scale molecular dynamics simulations have proprietary software to analyze various other properties resulting from the simulations, sometimes in shareware or other forms of limited access to the community, and sometimes limited in scope and use to some specific packages. Sophisticated algorithms to extract information about interatomic bonding, geometrical patterns, and thermodynamics are developed and implemented in some of these packages3,4,5,6,7, etc.
Here we propose the UMD package -&#160;an open-source package written in Python to analyze the output of molecular dynamics simulations. The UMD package allows for the computation of a wide range of structural, dynamical, and thermodynamical properties (Figure 1). The package is available via the GitHub website (https://github.com/rcaracas/UMD_package) and via a dedicated page (http://moonimpact.eu/umd-package/) of the ERC IMPACT project as an open-access package.
To make it universal and easier to handle, our approach is to first extract all the information related to the thermodynamic state and the atomic trajectories from the output file of the actual molecular-dynamics run. This information is stored in a dedicated file, whose format is independent of the original MD package where the simulation was run. We name these files &#8220;umd&#8221; files, which stands for Universal Molecular Dynamics. In this way, our UMD package can be easily used by any ab initio group with any software, all with a minimum effort of adaptation. The only requirement to use the present package is to write the appropriate parser from the output of the particular MD software into the umd file format, if this is not yet existent. For the time being, we provide such parsers for the VASP8 and the QBox9 packages.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61534/61534fig01.jpg" /> 
Figure 1: Flowchart of the UMD library. 
Physical properties are in blue, and major Python scripts and their options are in red. <a href="https://www.jove.com/files/ftp_upload/61534/61534fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The umd files are ASCII files; typical extension is &#8220;umd.dat&#8221; but not mandatory. All the analysis components can read ASCII files of the umd format, regardless of the actual name extension. However, some of the automatic scripts designed to perform fast large-scale statistics over several simulations specifically look for files with the umd.dat extension. Each physical property is expressed on one line. Every line starts with a keyword. In this way the format is highly adaptable and allows for new properties to be added to the umd file, all the while preserving its readability throughout versions. The first 30 lines of the umd file of the simulation of pyrolite at 4.6 GPa and 3000 K, used below in the discussion, are shown in Figure 2.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61534/61534fig02.jpg" /> 
Figure 2: The beginning of the umd file describing the simulation of liquid pyrolite at 4.6 GPa and 3000 K. 
The header is followed by the description of each snapshot. Each property is written on one line, containing the name of the physical property, the value(s), and the units, all separated by spaces. <a href="https://www.jove.com/files/ftp_upload/61534/61534fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
All umd files contain a header describing the content of the simulation cell: the number of atoms, electrons, and atomic types, as well as details for each atom, such as its type, chemical symbol, number of valence electrons, and its mass. An empty line marks the end of the header and separates it from the main part of the umd file.
Then each step of the simulation is detailed. First, the instantaneous thermodynamic parameters are given, each on a different line, specifying (i) the name of the parameter, like energy, stresses, equivalent hydrostatic pressure, density, volume, lattice parameters, etc., (ii) its value(s), and (iii) its units. A table describing the atoms comes next. A header line gives the different measures, like Cartesian positions, velocities, charges, etc., and their units. Then each atom is detailed on one line. By groups of three, corresponding to the three x, y, z axes, the entries are: the reduced positions, the Cartesian positions folded into the simulation cell, the Cartesian positions (that properly take into account the fact that atoms can traverse several unit cells during a simulation), the atomic velocities, and the atomic forces. The last two entries are scalars: charge and magnetic moment.
Two major libraries ensure the proper functioning of the entire package. The umd_process.py library deals with the umd files, like reading and printing. The crystallography.py library deals with all the information related to the actual atomic structure. The underlying philosophy of the crystallography.py library is to treat the lattice as a vectorial space. The unit cell parameters together with their orientation represent the basis vectors. The &#8220;Space&#8221; has a series of scalar attributes (specific volume, density, temperature, and specific number of atoms), thermodynamic properties (internal energy, pressure, heat capacity, etc.), and a series of tensorial properties (stress and elasticity). Atoms populate this space. The &#8220;Lattice&#8221; class defines this ensemble, alongside various few short calculations, like specific volume, density, obtaining the reciprocal lattice from the direct one, etc. The &#8220;Atoms&#8221; class defines the atoms. They are characterized by a series of scalar properties (name, symbol, mass, number of electrons, etc.) and a series of vectorial properties (the position in space, either relative to the vectorial basis described in the Lattice class, or relative to universal Cartesian coordinates, velocities, forces, etc.). Apart from these two classes, the crystallography.py library contains a series of functions to perform a variety of tests and calculations, such as atomic distances, or cell multiplication. The periodic table of the elements is also included as a dictionary.
The various components of the umd package write several output files. As a general rule, they are all ASCII files, all their entries are separated by tabs, and they are made as self-explanatory as possible. For example, they always clearly indicate the physical property and its units. The umd.dat files fully comply with this rule.

<table>
	<tbody>
		<tr>
			<td>getopt library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>glob library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>matplotlib library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>numpy library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>os library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>Python software</td>
			<td>The Python Software Foundation</td>
			<td>Version 2 and 3</td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>random library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>re library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>scipy library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>subprocess library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
		<tr>
			<td>sys library</td>
			<td></td>
			<td></td>
			<td>open-source</td>
		</tr>
	</tbody>
</table>

analyzing melts and fluids from ab initio molecular dynamics simulations with the umd package

We have developed a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts, water-based fluids, and various supercritical fluids. The package is a collection of Python scripts that include two major libraries dealing with file formats and with crystallography. All the scripts are run at the command line. We propose a simplified format to store the atomic trajectories and relevant thermodynamic information of the simulations, which is saved in UMD files, standing for Universal Molecular Dynamics. The UMD package allows the computation of a series of structural, transport and thermodynamic properties. Starting with the pair-distribution function it defines bond lengths, builds an interatomic connectivity matrix, and eventually determines the chemical speciation. Determining the lifetime of the chemical species allows running a full statistical analysis. Then dedicated scripts compute the mean-square displacements for the atoms as well as for the chemical species. The implemented self-correlation analysis of the atomic velocities yields the diffusion coefficients and the vibrational spectrum. The same analysis applied on the stresses yields the viscosity. The package is available via the GitHub website and via its own dedicated page of the ERC IMPACT project as open-access package.

Pyrolite is a model multi-component silicate melt (0.5Na2O 2CaO 1.5Al2O3 4FeO 30MgO 24SiO2) that best approximates the composition of the bulk silicate Earth&#8212;the geochemical average or our entire planet, except for its iron-based core19. The early Earth was dominated by a series of large-scale melting events20, the last one might have engulfed the entire planet, after its condensation for the protolunar disk21. Pyrolite represents the best approximant to the composition of such planetary-scale magma oceans. Consequently, we extensively studied the physical properties of pyrolite melt in the 3,000&#8210;5,000 K temperature range and 0&#8210;150 GPa pressure range from ab initio molecular-dynamics simulations in the VASP implementation. These thermodynamic conditions entirely characterize the Earth&#8217;s most extreme magma ocean conditions. Our study is an excellent example of a successful use of the UMD package for the entire in-depth analysis of the melts22. We computed the distribution and the average bond lengths, we traced the changes in cation-oxygen coordination, and compared our results to previous experimental and computational studies on amorphous silicates of various compositions. Our in-depth analysis helped decompose standard coordination numbers into their basic constituents, outline the presence of exotic coordination polyhedra in the melt, and extract lifetimes for all the coordination polyhedra. It also outlined the importance of sampling in simulations in terms of both length of the trajectory and also number of atoms present in the system that is modeled. As for post-processing, the UMD analysis is independent of these factors, however, they should be taken into account when interpreting the results provided by the UMD package. Here, we show a few examples of how the UMD package can be used to extract several characteristic features of the melts, with an application to molten pyrolite.
The Si-O pair distribution function obtained from the gofrs_umd.py script shows that the radius of the first coordination sphere, which is the first minimum of the g(r) function, lies around 2.5 angstroms at T = 3000 K and P = 4.6 GPa. The maximum of the g(r) lies at 1.635 &#197;&#8212;this is the best approximation to the bend length. The long tail is due to the temperature. Using this limit as the Si-O bond distance, the speciation analysis shows that SiO4 units, which can last for up to a few picoseconds, dominate the melt (Figure 5). There is an important part of the melt that shows partial polymerization, as reflected by the presence of dimers like Si2O7, and trimers like Si3Ox units. Their corresponding lifetime is in the order of the picosecond. Higher-order polymers all have considerably shorter lifetime.
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/61534/61534fig05.jpg" /> 
Figure 5: Lifetime of the Si-O chemical species. 
The speciation is identified in a multi-component melt at 4.6 GPa and 3000 K. The labels mark the SiO3, SiO4, and SiO5 monomers and the various SixOy polymers. <a href="https://www.jove.com/files/ftp_upload/61534/61534fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The different values of the vertical and horizontal steps, defined by the &#8211;z and &#8211;v flags above, yield various samplings of the MSD (Figure 6). Even large values of z and v are enough to define the slopes and thus the diffusion coefficients of the different atoms. The gain in time for the post-processing is remarkable when going to large values of z and v. The MSD offers a very strong validation criterion for the quality of the simulations. If the diffusion part of the MSD is not sufficiently long, that is a sign that the simulation is too short, and fails to reach the fluid state in a statistical sense. The minimum requirement for the diffusive part of the MSD highly depends on the system. One can require that all the atoms change their site at least once in the structure of the melt in order for it to be considered as a fluid10. An excellent example with applications in planetary sciences is complex silicate melts at high pressures close to or even below their liquidus line11. The Si atoms, the major network-forming cations, switch sites after more than two dozen picoseconds. Simulations shorter than this threshold would be considerably under-sampling the possible configurational space. However, as the coordinating anions, namely the O atoms, move faster than the central Si atoms, they can compensate for part of the slow mobility of Si. As such, the entire system could indeed cover a better sampling of the configurational space than assumed only from the Si displacements.
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/61534/61534fig06.jpg" /> 
Figure 6: Mean-square displacements (MSD). 
The MSD are illustrated for a few atomic types of a multi-component silicate melt. The sampling with various horizontal and vertical steps, z and v, yields consistent results. Solid circles: -z 50 &#8211;v 50. Open circles: -z 250 &#8211;v 500. <a href="https://www.jove.com/files/ftp_upload/61534/61534fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Finally, the atomic VAC functions yield the vibrational spectrum of the melt. Figure 7 shows the spectrum at the same pressure and temperature conditions as above. We represent the contributions of Mg, Si, and O atoms, as well as the total value. At zero frequency there is a finite value of the spectrum, which corresponds to the diffusion character of the melt. Extraction of the thermodynamic properties from the vibrational spectrum needs to remove this gas-like diffusive character from zero but also to properly take into account its decay at higher frequencies.
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/61534/61534fig07.jpg" /> 
Figure 7: The vibrational spectrum of pyrolite melt. 
The real part of the Fourier transform of the atomic velocity-velocity self-correlation function yields the vibrational spectrum. Here the spectrum is computed for a multi-component silicate melt. Fluids have a non-zero gas-like diffusive character at zero frequency. <a href="https://www.jove.com/files/ftp_upload/61534/61534fig07large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package at JoVE.com

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).

We have developed a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package ...

analyzing-melts-fluids-from-ab-initio-molecular-dynamics-simulations

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4.3K Views.  CNRS. Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).

Video: Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Isolation and Chemical Characterization of Lipid A from Gram-negative Bacteria

Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS can be subdivided into three domains: the distal O-polysaccharide, a core oligosaccharide, and the lipid A domain consisting of a lipid A molecular species and 3-deoxy-D-manno-oct-2-ulosonic acid residues (Kdo). The lipid A domain is the only component essential for bacterial cell survival. Following its synthesis, lipid A is chemically modified in response to environmental stresses such as pH or temperature, to promote resistance to antibiotic compounds, and to evade recognition by mediators of the host innate immune response. The following protocol details the small- and large-scale isolation of lipid A from gram-negative bacteria. Isolated material is then chemically characterized by thin layer chromatography (TLC) or mass-spectrometry (MS). In addition to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS, we also describe tandem MS protocols for analyzing lipid A molecular species using electrospray ionization (ESI) coupled to collision induced dissociation (CID) and newly employed ultraviolet photodissociation (UVPD) methods. Our MS protocols allow for unequivocal determination of chemical structure, paramount to characterization of lipid A molecules that contain unique or novel chemical modifications. We also describe the radioisotopic labeling, and subsequent isolation, of lipid A from bacterial cells for analysis by TLC. Relative to MS-based protocols, TLC provides a more economical and rapid characterization method, but cannot be used to unambiguously assign lipid A chemical structures without the use of standards of known chemical structure. Over the last two decades isolation and characterization of lipid A has led to numerous exciting discoveries that have improved our understanding of the physiology of gram-negative bacteria, mechanisms of antibiotic resistance, the human innate immune response, and have provided many new targets in the development of antibacterial compounds.

Isolation and characterization of the lipid A domain of lipopolysaccharide (LPS) from gram-negative bacteria provides insight into cell surface based mechanisms of antibiotic resistance, bacterial survival and fitness, and how chemically diverse lipid A molecular species differentially modulate host innate immune responses.

Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS ...

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique amino acid sequence, it is only realized by the folding of the polypeptide chain into a single defined three-dimensional arrangement or more commonly into an ensemble of interconverting conformations. Investigating the connection between protein conformation and its function is therefore essential for a complete understanding of how proteins are able to fulfill their great variety of tasks. One possibility to study conformational changes a protein undergoes while progressing through its functional cycle is hydrogen-1H/2H-exchange in combination with high-resolution mass spectrometry (HX-MS). HX-MS is a versatile and robust method that adds a new dimension to structural information obtained by e.g. crystallography. It is used to study protein folding and unfolding, binding of small molecule ligands, protein-protein interactions, conformational changes linked to enzyme catalysis, and allostery. In addition, HX-MS is often used when the amount of protein is very limited or crystallization of the protein is not feasible. Here we provide a general protocol for studying protein dynamics with HX-MS and describe as an example how to reveal the interaction interface of two proteins in a complex. &#160;&#160;

Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique ...

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This flexible tool offers a detailed observation of chemical gas-phase kinetics in reacting flows under well-controlled conditions. The vast range of operating conditions available in a laminar flow reactor enables access to extraordinary combustion applications that are typically not achievable by flame experiments. These include rich conditions at high temperatures relevant for gasification processes, the peroxy chemistry governing the low temperature oxidation regime or investigations of complex technical fuels. The presented setup allows measurements of quantitative speciation data for reaction model validation of combustion, gasification and pyrolysis processes, while enabling a systematic general understanding of the reaction chemistry. Validation of kinetic reaction models is generally performed by investigating combustion processes of pure compounds. The flow reactor has been enhanced to be suitable for technical fuels (e.g. multi-component mixtures like Jet A-1) to allow for phenomenological analysis of occurring combustion intermediates like soot precursors or pollutants. The controlled and comparable boundary conditions provided by the experimental design allow for predictions of pollutant formation tendencies. Cold reactants are fed premixed into the reactor that are highly diluted (in around 99 vol% in Ar) in order to suppress self-sustaining combustion reactions. The laminar flowing reactant mixture passes through a known temperature field, while the gas composition is determined at the reactors exhaust as a function of the oven temperature. The flow reactor is operated at atmospheric pressures with temperatures up to 1,800 K. The measurements themselves are performed by decreasing the temperature monotonically at a rate of -200 K/h. With the sensitive MBMS technique, detailed speciation data is acquired and quantified for almost all chemical species in the reactive process, including radical species.

An investigation of the oxidative combustion chemistry of novel biofuels, fuel components, or jet fuels by comparison of quantitative speciation data is presented. The data can be used for kinetic model validation and enables fuel assessment strategies.This manuscript describes the atmospheric high-temperature flow reactor and demonstrates its capabilities.

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This ...

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-&#197;ngstr&#246;m spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Here, we present a protocol to investigate the structure and dynamics of interfacial water at the atomic scale, in terms of submolecular resolution imaging, molecular manipulation, and single-bond vibrational spectroscopy.

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal ...

A Closed-Type Wireless Nanopore Electrode for Analyzing Single Nanoparticles

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in nanoscience. However, electrochemically analyzing single nanoparticles is challenging, as the sensing nanointerface is uncontrollable. To address this challenge, we describe here the fabrication and characterization of a closed-type wireless nanopore electrode (WNE) that exhibits a highly controllable morphology and outstanding reproducibility. The facile fabrication of WNE enables the preparation of well-defined nanoelectrodes in a general chemistry laboratory without the use of a clean room and expensive equipment. One application of a 30 nm closed-type WNE in analysis of single gold nanoparticles in the mixture is also highlighted, which shows a high current resolution of 0.6 pA and high temporal resolution of 0.01 ms. Accompanied by their excellent morphology and small diameters, more potential applications of closed-type WNEs can be expanded from nanoparticle characterization to single molecule/ion detection and single-cell probing.

Here, we present a protocol for fabrication of a closed-type wireless nanopore electrode and subsequent electrochemical measurement of single nanoparticle collisions.

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in ...

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

A significant number of heterogeneously-catalyzed chemical processes occur under liquid conditions, but simulating catalyst function under such conditions is challenging when it is necessary to include the solvent molecules. The bond breaking and forming processes modeled in these systems necessitate the use of quantum chemical methods. Since molecules in the liquid phase are under constant thermal motion, simulations must also include configurational sampling. This means that multiple configurations of liquid molecules must be simulated for each catalytic species of interest. The goal of the protocol presented here is to generate and sample trajectories of configurations of liquid water molecules around catalytic species on flat transition metal surfaces in a way that balances chemical accuracy with computational expense. Specifically, force field molecular dynamics (FFMD) simulations are used to generate configurations of liquid molecules that can subsequently be used in quantum mechanics-based methods such as density functional theory or ab initio molecular dynamics. To illustrate this, in this manuscript, the protocol is used for catalytic intermediates that could be involved in the pathway for the decomposition of glycerol (C3H8O3). The structures that are generated using FFMD are modeled in DFT in order to estimate the enthalpies of solvation of the catalytic species and to identify how H2O molecules participate in catalytic decompositions.

The goal of the protocol presented here is to generate and sample trajectories of configurations of liquid water molecules around catalytic species on a flat transition metal surface. The sampled configurations can be used as starting structures in quantum mechanics-based methods.

A significant number of heterogeneously-catalyzed chemical processes occur under liquid conditions, but simulating catalyst function under such conditions ...

Developing Photosensitizer-Cobaloxime Hybrids for Solar-Driven H2 Production in Aqueous Aerobic Conditions

Developing photocatalytic H2 production devices is the one of the key steps for constructing a global H2-based renewable energy infrastructure. A number of photoactive assemblies have emerged where a photosensitizer and cobaloxime-based H2 production catalysts work in tandem to convert light energy into the H-H chemical bonds. However, the long-term instability of these assemblies and the need for hazardous proton sources have limited their usage. Here, in this work, we have integrated a stilbene-based organic dye into the periphery of a cobaloxime core via a distinct axial pyridine linkage. This strategy allowed us to develop a photosensitizer-catalyst hybrid structure with the same molecular framework. In this article, we have explained the detailed procedure of the synthesis of this hybrid molecule in addition to its comprehensive chemical characterization. The structural and optical studies have exhibited an intense electronic interaction between the cobaloxime core and the organic photosensitizer. The cobaloxime was active for H2 production even in the presence of water as the proton source. Here, we have developed a simple airtight system connected with an online H2 detector for the investigation of the photocatalytic activity by this hybrid complex. This photosensitizer-catalyst dyad present in the experimental setup continuously produced H2 once it was exposed in the natural sunlight. This photocatalytic H2 production by the hybrid complex was observed in aqueous/organic mixture media in the presence of a sacrificial electron donor under complete aerobic conditions. Thus, this photocatalysis measurement system along with the photosensitizer-catalyst dyad provide valuable insight for the development of next generation photocatalytic H2 production devices.

Developing Photosensitizer-Cobaloxime Hybrids for Solar-Driven H2 Production in Aqueous Aerobic Conditions

We have directly incorporated a stilbene-based organic dye into a cobaloxime core to generate a photosensitizer-catalyst dyad for photocatalytic H2 production. We have also developed a simple experimental setup for evaluating the light-driven H2 production by photocatalytic assemblies.

Developing photocatalytic H2 production devices is the one of the key steps for constructing a global H2-based renewable energy infrastructure. A number ...

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

The accurate molecular simulation prediction of vibrational spectra, and other structural, energetic and spectral characteristics, of photo-active metal-oxide surfaces in contact with light-absorbing dyes is an ongoing thorny and elusive challenge in physical chemistry. With this in mind, a molecular-dynamics (MD) simulation were performed by using optimized empirical potentials for a well-representative and prototypical dye-sensitized solar cell (DSC) solvated by a widely-studied room temperature ionic liquid (RTIL), in the guise of a [bmim]+[NTf2]- RTIL solvating an N719-sensitizing dye adsorbed onto 101 anatase-titania. In doing so, important insights were gleaned into how using a RTIL as the electrolytic hole acceptor modulates the dynamical and vibrational properties of a N719 dye, estimating the spectra for the DSC photo-active interface via Fourier transformation of mass-weighted velocity autocorrelation functions from MD. The acquired vibrational spectra were compared with the experiment spectra and those sampled from ab initio molecular dynamics (AIMD); in particular, various empirical-potential spectra generated from MD provide insight into how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction. In any event, careful fitting of empirical force-field models has been shown to be an effective tool in handling DSC vibrational properties, when validated by AIMD and an experiment.

A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.

The accurate molecular simulation prediction of vibrational spectra, and other structural, energetic and spectral characteristics, of photo-active ...

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions.

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

The atmospheric concentrations of weakly bound molecular clusters can be computed from the thermochemical properties of low energy structures found through a multi-step configurational sampling methodology utilizing a genetic algorithm and semi-empirical and ab initio quantum chemistry.

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas ...

Interactive Molecular Model Assembly with 3D Printing

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical laboratories and chemical education. Building on the long and successful history of physical modeling of molecular systems, we present select models along with a protocol to facilitate 3D printing of molecular structures that are able to do more than represent shape and connectivity. Models assembled as described incorporate dynamic aspects and degrees of freedom into saturated hydrocarbon structures. As a representative example, cyclohexane was assembled from parts printed and finished using different thermoplastics, and the resulting models retain their functionality at a variety of scales. The resulting structures show configurational space accessibility consistent with calculations and literature, and versions of these structures can be used as aids to illustrate concepts that are difficult to convey in other ways. This exercise enables us to evaluate successful printing protocols, make practical recommendations for assembly, and outline design principles for physical modeling of molecular systems. The provided structures, procedures, and results provide a foundation for individual manufacture and exploration of molecular structure and dynamics with 3D printing.

Physical modeling of microscopic systems helps obtain insights that are difficult to gain by other means. To facilitate the construction of physical molecular models, we demonstrate how 3D printing can be used to assemble functional macroscopic models that capture qualities of molecular systems in a tactile way.

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical ...