Molecular dynamics simulation of single pulse discharge process: clarifying the function of pressure generated inside the melting area in EDM

Due to the unique and superior properties of using thermal energy to machine electrically conductive material regardless of its hardness, electrical discharge machining has been widely used and has become indispensable in the manufacturing industry. However, the incompleteness and imperfection of the fundamental theory behind it seriously hinders its further application and development. In this work, a single pulse discharge in deionised water was simulated to study the material removal motivity and mechanisms with molecular dynamics simulations. The results show that during the discharge process, there exists a decreasing pressure gradient along the depth direction towards the surface of the melting area. When the pressure gradient overcomes the atomic bonding forces, the melting material can be ablated from the electrode. Thus, it is not the case that the melting material cannot be removed during the discharge process; material removal occurs throughout the whole discharge process. In addition, it was found that the bulge is formed for two reasons: the main reason is the shearing flow of the melting material caused by the pressure gradient along the radial direction in the melting area, and the other is the accumulation of the spattering material from the opposite electrode.     

Specific features of a single-pulse sliding discharge in neon near the threshold for spark breakdown

Experimental data on the spatial structure of a single-pulse sliding discharge in neon at voltages below, equal to, and above the threshold for spark breakdown are discussed. The experiments were carried at gas pressures of 30 and 100 kPa and different polarities of the discharge voltage. Photographs of the plasma structure in two discharge chambers with different dimensions of the discharge zone and different thicknesses of an alumina dielectric plate on the surface of which the discharge develops are inspected. Common features of the prebreakdown discharge and its specific features depending on the voltage polarity and gas pressure are analyzed. It is shown that, at voltages below the threshold for spark breakdown, a low-current glow discharge with cathode and anode spots develops in the electrode gap. Above the breakdown threshold, regardless of the voltage polarity, spark channels directed from the cathode to the anode develop against the background of a low-current discharge.     

Development of a spark sustained by charging the stray capacitance of the external circuit in atmospheric-pressure nitrogen

Results are presented from experimental studies and numerical simulations of a spark discharge excited in a short point-plane gap filled with atmospheric-pressure nitrogen. The discharge was powered from a high-voltage source connected to the discharge gap through a large ballast resistance. In this case, a short-term spark develops only due to the charging of the stray capacitance of the external circuit; therefore, the energy released by the spark and its intensity are both low. Rapid current growth in a weak spark is accompanied by the contraction of the current channel rather than by its gasdynamic expansion, as it occurs in long-duration kiloampere sparks. Simulations show that, because of the very short spark lifetime, the plasma in a weak spark is substantially nonequilibrium and the gas temperature is fairly high.     

Evolution of the radial structure of a negative corona during its transformation into a glow discharge and a spark

With the proper stabilization of a negative corona, it is possible to increase the threshold current at which the corona discharge in the point-plane gap in air transforms into a spark. Then, in the current range corresponding to the transition region between the corona discharge and the spark, a new type of discharge arises—an atmospheric-pressure diffuse glow discharge. The transformation of the negative corona into a glow discharge and then into a spark is accompanied by the rearrangement of the discharge structure. The experiments show that, as the corona current increases, the radial current profile at the anode shrinks and the glow diameter near the anode increases. The radial profiles of the current and the corona glow during the transition to a glow discharge are measured. The longitudinal structure of the corona is computed using a 1.5-dimensional model that, unlike the other available models, includes gas ionization in the drift region of the corona. The experimental data are used to determine the effective cross section of the current channel at the anode. The radial glow profile near the anode is calculated using the measured current profile and assuming that the field profile is parabolic.     

Acceleration of ions in a beam-plasma discharge in a low magnetic field: Interrelation between the electron and ion energy distributions

Previous experiments revealed the effect of stable acceleration of ions in a plasma-beam discharge in a low magnetic field to energies one order of magnitude higher than the electron thermal energy. To verify the previously proposed mechanisms for this effect, the velocity distribution function of the electrons arriving at the collector and the energy distribution of the ions escaping from the discharge transversely to the axis were measured. It is found that ion acceleration is accompanied by significant electron heating near the discharge axis. The time behavior and longitudinal profile of the intensity of the excited high-frequency oscillations in the frequency range ω ～ ω _pe were studied. The accumulation of regular oscillations in the beam-injection region and their stochastization during the propagation along the system axis were observed. The experimental results correlate qualitatively with the data of previous numerical simulations.     

Doses for experiments with microbeams and microcrystals: Monte Carlo simulations in RADDOSE‐3D

Increasingly, microbeams and microcrystals are being used for macromolecular crystallography (MX) experiments at synchrotrons. However, radiation damage remains a major concern since it is a fundamental limiting factor affecting the success of macromolecular structure determination. The rate of radiation damage at cryotemperatures is known to be proportional to the absorbed dose, so to optimize experimental outcomes, accurate dose calculations are required which take into account the physics of the interactions of the crystal constituents. The program RADDOSE‐3D estimates the dose absorbed by samples during MX data collection at synchrotron sources, allowing direct comparison of radiation damage between experiments carried out with different samples and beam parameters. This has aided the study of MX radiation damage and enabled prediction of approximately when it will manifest in diffraction patterns so it can potentially be avoided. However, the probability of photoelectron escape from the sample and entry from the surrounding material has not previously been included in RADDOSE‐3D, leading to potentially inaccurate does estimates for experiments using microbeams or microcrystals. We present an extension to RADDOSE‐3D which performs Monte Carlo simulations of a rotating crystal during MX data collection, taking into account the redistribution of photoelectrons produced both in the sample and the material surrounding the crystal. As well as providing more accurate dose estimates, the Monte Carlo simulations highlight the importance of the size and composition of the surrounding material on the dose and thus the rate of radiation damage to the sample. Minimizing irradiation of the surrounding material or removing it almost completely will be key to extending the lifetime of microcrystals and enhancing the potential benefits of using higher incident X‐ray energies.     

Simulation of nonstationary phenomena in atmospheric-pressure glow discharge

Nonstationary processes in atmospheric-pressure glow discharge manifest themselves in spontaneous transitions from the normal glow discharge into a spark. In the experiments, both so-called completed transitions in which a highly conductive constricted channel arises and incomplete transitions accompanied by the formation of a diffuse channel are observed. A model of the positive column of a discharge in air is elaborated that allows one to interpret specific features of the discharge both in the stationary stage and during its transition into a spark and makes it possible to calculate the characteristic oscillatory current waveforms for completed transitions into a spark and aperiodic ones for incomplete transitions. The calculated parameters of the positive column in the glow discharge mode agree well with experiment. Data on the densities of the most abundant species generated in the discharge (such as atomic oxygen, metastable nitrogen molecules, ozone, nitrogen oxides, and negative oxygen ions) are presented.     

Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd

The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of the microtubule motor, ncd, from the open conformation to the closed conformation seen in myosin. MD simulations were done of both the open and the closed conformations, with either MgADP or MgATP at the active site. All MD structures were stable at 300 K for 500 ps, implying that the open and closed conformers all represented local minima on a global free energy surface. Free energy calculations indicated that the open structure was energetically favored with MgADP at the active site, suggesting why only the open structure has been captured in crystallographic work. With MgATP, the closed and open structures had roughly equal energies. Simulated annealing MD showed the transformation from the closed phosphate-tube ncd structure to an open configuration. The MD simulations also showed that the coordination of switch 1 to the nucleotide dramatically affected the position of both the bound nucleotide and switch 2 and that a closed phosphate-tube may be necessary for catalysis.     

A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals

Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules.     

On the relation between the index of the interelectrode gap filling with spark channels and the current of a pulsed multichannel sliding discharge in Ne,Ar, and Xe

Experimental results and model concepts concerning the relation between the index K of the interelectrode gap filling with spark channels and the peak current I _peak of a single-pulse submicrosecond multichannel complete sliding discharge on an alumina ceramic surface are discussed. The spatial structure of an incomplete discharge at the threshold for the surface spark breakdown of gas is considered. The experiments were performed with three gases, Ne, Ar, and Xe, at pressures of 30 and 100 kPa and opposite polarities of the discharge voltage, with two discharge chambers differing in the geometry of the discharge gap and the thickness of the ceramic plate. It is shown that, although the structure of the incomplete discharge at the threshold for spark breakdown varies from diffuse homogeneous to pronounced filamentary, the dependence \(K\left( {\sqrt[6]{{I_{peak} }}} \right)\) for a complete discharge is close to linear and can be qualitatively explained by the earlier proposed semiempirical model of the time evolution of the structure of a multichannel discharge. In particular, the estimated steepness of the dependence \(K\left( {\sqrt[6]{{I_{peak} }}} \right)\) agrees best with the experimental results when the local density of free electrons at the threshold for spark breakdown is 10¹⁶ cm^?3 or higher.     

Structure,stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)3]) cyclic peptide nanotube: a molecular dynamics study

The structural stability of 8 × ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube (CPN) in water and different phospholipid bilayers were explored by 100 ns independent molecular dynamics (MD) simulations. The role of non-bonded interaction energy between the side and main chains of cyclic peptide rings in different membrane environments assessed, wherein the repulsive electrostatic interaction energy between neighbouring cyclic peptide rings was found adequate to break hydrogen bond energy thereby to crumple CPN. Further, the water permeation across the CPN channel was studied in four types of phospholipid bilayers- DMPG (1,2-Dimyristoyl-sn-glycero-3-phosphorylglycerol), DMPS (1,2-Dimyristoyl-sn-glycero-3-phosphoserine), POPC (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPE (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) from MD simulations. DMPS membrane shows higher non-bonded interaction energies (?1913.06 kJ/mol of electrostatic interaction energy and ?994.13 kJ/mol of van der Waals interaction energy) with CPN due to the presence of polar molecules in lipid structure. Thusly, the non-bonded interaction energies were essential towards the stability of CPN than hydrogen bonds between the nearby cyclic peptides. The result also reveals the role of side chains, hydrogen bonds and non-bonded interaction energies in an aqueous environment. The diffusion coefficient of water obtained from means square deviation calculation shows similar coefficients irrespective of the lipid surroundings. However, the permeation coefficients demonstrate water flow in the channel relies upon the environment.     

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single‐state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on‐ or off‐target models of the native protein fold and could be used in future studies to design for desired properties other than stability. Proteins 2014; 82:771–784. © 2013 Wiley Periodicals, Inc.     

Radio-frequency discharge in a molecular gas flow at a frequency of 1.76 MHz

Results are presented from experiments on the initiation of a homogeneous stable capacitive RF discharge at a frequency of 1.76 MHz in a high-speed molecular gas flow between metal electrodes at a pressure of 5 Torr or dielectric-coated electrodes at a pressure of up to 50 Torr. A mechanism of the current closure in the electrode sheaths related to the primary photoelectric current generated alternately from different electrodes is proposed. The average electron energy increases via second-kind (superelastic) collisions, and fast electrons with energies corresponding to the amplitude value of the RF voltage appear in the electron energy spectrum. As a result, primary emission arises due to the excitation of emitting states from metastable molecular levels. The primary photoelectric current initiates electron avalanches in the electrode sheaths due to secondary photoelectron emission. According to calculations, the current?voltage characteristic of the sheath in this type of discharge is ascending and the field strengths in the electrode sheath and positive column are lower than those in a self-sustained dc discharge. The calculated results are compared with the experimental data.     

Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy

Molecular dynamics (MD) simulations have been performed on the A6 containing DNA dodecamers d(GGCAAAAAACGG) solved by NMR and d(CGCAAAAAAGCG) solved by crystallography. The experimental structures differ in the direction of axis bending and in other small but important aspects relevant to the DNA curvature problem. Five nanosecond MD simulations of each sequence have been performed, beginning with both the NMR and crystal forms as well as canonical B-form DNA. The results show that all simulations converge to a common form in close proximity to the observed NMR structure, indicating that the structure obtained in the crystal is likely a strained form due to packing effects. A-tracts in the MD model are essentially straight. The origin of axis curvature is found at pyrimidine-purine steps in the flanking sequences.     

Evolution of the channel of a long leader in air after a sharp decrease in the discharge current

The dynamics of the plasma parameters in a given cross section of a long-lived leader channel in air after a jumplike decrease in the discharge current is simulated numerically with the help of a one-dimensional non-steady-state model constructed with allowance for the dynamics of the energy input into the channel, the expansion of the channel, and the nonequilibrium ionization kinetics in the leader plasma. It is shown that, after a decrease in the current, the electric field in the channel, first, rapidly decreases and, then, increases gradually as the gas cools. The higher the energy input into the discharge before the decrease in the current, the longer the time scale on which the electric field increases. The results of simulations of the electric field in the channel agree with the data from the experimental modeling of the actual leader channel by a short spark.     

Numerical simulations of spark channels propagating along the ground surface: Comparison with high-current experiment

A numerical model of a spark discharge propagating along the ground surface from the point at which an ∼100-kA current pulse is input into the ground has been developed based on experiments in which the velocity of a long leader was measured as a function of the leader current. The results of numerical simulations are in good agreement with the measured characteristics of creeping discharges excited in field experiments by using a high-power explosive magnetic generator. The reason why the length of a spark discharge depends weakly on the number of simultaneously developing channels is found. Analysis of the influence of the temporal characteristics of the current pulse on the parameters of the creeping spark discharge shows that actual lighting may exhibit similar behavior.     

The crystal and molecular structures of cellulose I and II

The paper describes molecular dynamics (MD) simulations on the crystal structures of the Iβ and II phases of cellulose. Structural proposals for each of these were made in the 1970s on the basis of X-ray diffraction data. However, due to the limited resolution of these data some controversies remained and details on hydrogen bonding could not be directly obtained. In contrast to structure factor amplitudes in X-ray diffraction, energies, as obtained from MD simulations, are very sensitive to the positions of the hydroxyl hydrogen atoms. Therefore the latter technique is very suitable for obtaining such structural details. MD simulations of the Iβ phase clearly shows preference for one of the two possible models in which the chains are packed in a parallel orientation. Only the parallel-down mode (in the definition of Gardner and Blackwell (1974) J Biopolym 13: 1975-2001) presents a stable structure. The hydrogen bonding consists of two intramolecular hydrogen bonds parallel to the glycosidic linkage for both chains, and two intralayer hydrogen bonds. The layers are packed hydrophobically. All hydroxymethyl group are positioned in the tg conformation. For the cellulose II form it was found that, in contrast to what seemed to emerge from the X-ray fibre diffraction data, both independent chains had the gt conformation. This idea already existed because of elastic moduli calculations and 13C-solid state NMR data. Recently, the structure of cellotetraose was determined. There appear to be a striking similarity between the structure obtained from the MD simulations and this cellotetraose structure in terms of packing of the two independent molecules, the hydrogen bonding network and the conformations of the hydroxymethyl group, which were also gt for both molecules. The structure forms a 3D hydrogen bonded network, and the contribution from electrostatics to the packing is more pronounced than in case of the Iβ structure. In contrast to what is expected, in view of the irreversible transition of the cellulose I to II form, the energies of the Iβ form is found to be lower than that of II by 1 kcal mol-1 per cellobiose. This revised version was published online in November 2006 with corrections to the Cover Date.     

Theoretical study of the surface properties of poly(dimethylsiloxane) and poly(tetrafluoroethylene)

Molecular dynamics (MD) simulations of poly(dimethylsiloxane) (PDMS) and poly(tetrafluoroethylene) (PTFE) were carried out to determine their surface properties and energies. This study helps to gain better insight into the molecular modeling of PDMS and PTFE, in particular how different approaches affect calculations of surface energy. Current experimental and theoretical data were used to further understand the surface properties of PDMS and PTFE as well as to validate and verify results obtained from the combination of density functional theory (DFT) calculations (including periodic boundary conditions) and MD simulations. Detailed analysis of the structure and electronic properties (by calculation of the projected density of states) of the bulk and surface models of PDMS and PTFE was performed. The sensitivity of the surface energy calculation of these two polymers to the chemistry and model preparation was indicated. The balance between the molecular density, weight (which also reflects bond orientation in the surface region), bond flexibility, and intramolecular interactions including bond stretching was revealed to govern the results obtained. In modeling, the structural organization of polymer near a given surface (types and number of end groups and broken bonds due to application of different cut offs of the periodic structure) also significantly affects the final results. Besides the structural differences, certain simulation parameters, such the DFT functionals and simulation boxes utilized, play an important role in determining surface energy. The models used here were shown to be sufficient due to their good agreement with experimental and other theoretical data related to surface properties and surface energies.     

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.     

A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics

A sample of 35 independent molecular dynamics (MD) simulations of calmodulin (CaM) equilibrium dynamics was prepared from different but equally plausible initial conditions (20 simulations of the wild-type protein and 15 simulations of the D129N mutant). CaM's radius of gyration and backbone mean-square fluctuations were analyzed for the effect of the D129N mutation, and simulations were compared with experiments. Statistical tests were employed for quantitative comparisons at the desired error level. The computational model predicted statistically significant compaction of CaM relative to the crystal structure, consistent with the results of small-angle X-ray scattering (SAXS) experiments. This effect was not observed in several previously reported studies of (Ca2+)(4)-CaM, which relied on a single MD run. In contrast to radius of gyration, backbone mean-square fluctuations showed a distinctly non-normal and positively skewed distribution for nearly all residues. Furthermore, the D129N mutation affected the backbone dynamics in a complex manner and reduced the mobility of Glu123, Met124, Ile125, Arg126, and Glu127 located in the adjacent alpha-helix G. The implications of these observations for the comparisons of MD simulations with experiments are discussed. The proposed approach may be useful in studies of protein equilibrium dynamics where MD simulations fall short of properly sampling the conformational space, and when the comparison with experiments is affected by the reproducibility of the computational model.