Comparison of forcefields for molecular dynamics simulations of hydrocarbon phase diagrams
Molecular dynamics calculations are performed to calculate vapor–liquid equilibrium of methane–n-butane mixture. Three force-field models are tested: the TraPPE-UA united-atom forcefield, LOPLS-AA all-atom forcefield and a fully flexible version of the TraPPEEH all-atom forcefield. All those forcefields reproduce well the composition of liquid phase in the mixture as a function of pressure at the 300 K isotherm, while significant discrepancies from experimental data are observed in the saturated vapor compositions with OPLS-AA and TraPPE-UA forcefields. The best agreement with the experimental phase diagram is found with TraPPE-EH forcefield which accurately reproduces compositions of both liquid and vapor phase. This forcefield can be recommended for simulation of two-phase hydrocarbon systems.
The method ofWave Packet Molecular Dynamics Method (WPMD) is a promising replacement of the classical molecular dynamics for the simulations of many-electron systems including nonideal plasmas. In this contribution we report on a packet splitting technique where an electron is represented by multiple Gaussians, with mixing coefficients playing the role of additional dynamic variables. It provides larger flexibility and better accuracy than the original WPMD with a single Gaussian per electron. As a test case we consider ionization of hydrogen atom in a short laser pulse, where the split packets provide a basis for quantum branching.
The wave packet molecular dynamics (WPMD) method provides a variational approximation to the solution of the time-dependent Schr¨odinger equation. Its application in the field of high-temperature dense plasmas has yielded diverging electron width (spreading), which results in diminishing electron-nuclear interactions. Electron spreading has previously been ascribed to a shortcoming of the WPMD method and has been counteracted by various heuristic additions to the models used. We employ more accurate methods to determine if spreading continues to be predicted by them and how WPMD can be improved. A scattering process involving a single dynamic electron interacting with a periodic array of statically screened protons is used as a model problem for comparison. We compare the numerically exact split operator Fourier transform method, the Wigner trajectory method, and the time-dependent variational principle (TDVP). Within the framework of the TDVP, we use the standard variational form of WPMD, the single Gaussian wave packet (WP), as well as a sum of Gaussian WPs, as in the split WP method. Wave packet spreading is predicted by all methods, so it is not the source of the unphysical diminishing of electron-nuclear interactions in WPMD at high temperatures. Instead, the Gaussian WP’s inability to correctly reproduce breakup of the electron’s probability density into localized density near the protons is responsible for the deviation from more accurate predictions. Extensions of WPMD must include a mechanism for breakup to occur in order to yield dynamics that lead to accurate electron densities.
Helical segments are common structural elements of membrane proteins. Dimerization and oligomerization of transmembrane (TM) α-helices provides the framework for spatial structure formation and protein-protein interactions. The membrane itself also takes part in the protein functioning. There are some examples of the mutual influence of the lipid bilayer properties and embedded membrane proteins. This work aims at the detail investigation of protein-lipid interactions using model systems: TM peptides corresponding to native protein segments. Three peptides were considered corresponding to TM domains of human glycophorin A (GpA), epidermal growth factor receptor (EGFR) and proposed TM-segment of human neuraminidase-1 (Neu1). A computational analysis of structural and dynamical properties was performed using molecular dynamics method. Monomers of peptides were considered incorporated into hydrated lipid bilayers. It was confirmed, that all these TM peptides have stable helical conformation in lipid environment, and the mutual adaptation of peptides and membrane was observed. It was shown that incorporation of the peptide into membrane results in the modulation of local and mean structural properties of the bilayer. Each peptide interacts with lipid acyl chains having special binding sites on the surface of central part of α-helix that exist for at least 200 ns. However, lipid acyl chains substitute each other faster occupying the same site. The formation of a special pattern of protein-lipid interactions may modulate the association of TM domains of membrane proteins, so membrane environment should be considered when proposing new substances targeting cell receptors.
This paper describes the surface environment of the dense plasma arcs that damage rf accelerators, tokamaks, and other high gradient structures. We simulate the dense, nonideal plasma sheath near a metallic surface using molecular dynamics (MD) to evaluate sheaths in the non-Debye region for high density, low temperature plasmas. We use direct two-component MD simulations where the interactions between all electrons and ions are computed explicitly. We find that the non-Debye sheath can be extrapolated from the Debye sheath parameters with small corrections. We find that these parameters are roughly consistent with previous particle-in-cell code estimates, pointing to densities in the range 10^24–10^25 m^3. The high surface fields implied by these results could produce field emission that would short the sheath and cause an instability in the time evolution of the arc, and this mechanism could limit the maximum density and surface field in the arc. These results also provide a way of understanding how the properties of the arc depend on the properties (sublimation energy, for example) of the metal. Using these results, and equating surface tension and plasma pressure, it is possible to infer a range of plasma densities and sheath potentials from scanning electron microscope images of arc damage. We find that the high density plasma these results imply and the level of plasma pressure they would produce is consistent with arc damage on a scale 100 nm or less, in examples where the liquid metal would cool before this structure would be lost. We find that the submicron component of arc damage, the burn voltage, and fluctuations in the visible light production of arcs may be the most direct indicators of the parameters of the dense plasma arc, and the most useful diagnostics of the mechanisms limiting gradients in accelerators.
Proof-of-concept results are presented on the application of molecular modeling and simulation to the gas extraction problems. Both hydrocarbon mixtures and gas hydrates in porous media are considered.
Plasmatic membranes contain high amount of membrane proteins. They perform vital functions of life, so any disruptions in their structure result in pathologies and diseases. Studies of these proteins with experimental methods are very complicated and expensive, as they require the membrane environment. Despite considerable progress achieved so far in methods of structure determination and property analysis, many computational methods are developing to predict the structural and dynamical parameters of proteins in membranes. Among the algorithms of modeling are the homology analysis, de novo structure prediction, molecular dynamics simulations and other. With growing computational capabilities, sophisticated techniques are developed taking into account more environmental factors. Combined approaches with different levels of approximation of intermolecular interactions are widely used. The major interest in studies of membrane proteins is focused on their transmembrane domains that are fundamental structural elements and are constituted by α-helices or helical bundles incorporated into lipid bilayer in most cases. Therefore, the fundamental problem of interaction of a pair of helices in membrane arises: the exact mechanism of this process is still not so clear. In place of the prevailing concept of dimerization motifs that states the importance of protein-protein contacts, a new model of the membrane as an adaptable lipid matrix is proposed. It states that biological membrane can adjust its properties around proteins and also modulates their activity. This mechanism of the mutual influence of two components is challenging modern computational methods of membrane model- ing because these systems are quite large and include many components to be treated accurately. Nowadays, investigations of the complex multi-component model systems become possible with modern methods of computational experiment.
The dynamics of a two-component Davydov-Scott (DS) soliton with a small mismatch of the initial location or velocity of the high-frequency (HF) component was investigated within the framework of the Zakharov-type system of two coupled equations for the HF and low-frequency (LF) fields. In this system, the HF field is described by the linear Schrödinger equation with the potential generated by the LF component varying in time and space. The LF component in this system is described by the Korteweg-de Vries equation with a term of quadratic influence of the HF field on the LF field. The frequency of the DS soliton`s component oscillation was found analytically using the balance equation. The perturbed DS soliton was shown to be stable. The analytical results were confirmed by numerical simulations.
Radiation conditions are described for various space regions, radiation-induced effects in spacecraft materials and equipment components are considered and information on theoretical, computational, and experimental methods for studying radiation effects are presented. The peculiarities of radiation effects on nanostructures and some problems related to modeling and radiation testing of such structures are considered.