Modelling vacuum arcs : from plasma initiation to surface interactions

A better understanding of vacuum arcs is desirable in many of today's 'big science' projects including linear colliders, fusion devices, and satellite systems. For the Compact Linear Collider (CLIC) design, radio-frequency (RF) breakdowns occurring in accelerating cavities influence efficiency optimisation and cost reduction issues. Studying vacuum arcs both theoretically as well as experimentally under well-defined and reproducible direct-current (DC) conditions is the first step towards exploring RF breakdowns. In this thesis, we have studied Cu DC vacuum arcs with a combination of experiments, a particle-in-cell (PIC) model of the arc plasma, and molecular dynamics (MD) simulations of the subsequent surface damaging mechanism. We have also developed the 2D Arc-PIC code and the physics model incorporated in it, especially for the purpose of modelling the plasma initiation in vacuum arcs. Assuming the presence of a field emitter at the cathode initially, we have identified the conditions for plasma formation and have studied the transitions from field emission stage to a fully developed arc. The 'footing' of the plasma is the cathode spot that supplies the arc continuously with particles; the high-density core of the plasma is located above this cathode spot. Our results have shown that once an arc plasma is initiated, and as long as energy is available, the arc is self-maintaining due to the plasma sheath that ensures enhanced field emission and sputtering. The plasma model can already give an estimate on how the time-to-breakdown changes with the neutral evaporation rate, which is yet to be determined by atomistic simulations. Due to the non-linearity of the problem, we have also performed a code-to-code comparison. The reproducibility of plasma behaviour and time-to-breakdown with independent codes increased confidence in the results presented here. Our MD simulations identified high-flux, high-energy ion bombardment as a possible mechanism forming the early-stage surface damage in vacuum arcs. In this mechanism, sputtering occurs mostly in clusters, as a consequence of overlapping heat spikes. Different-sized experimental and simulated craters were found to be self-similar with a crater depth-to-width ratio of about 0.23 (sim) - 0.26 (exp). Experiments, which we carried out to investigate the energy dependence of DC breakdown properties, point at an intrinsic connection between DC and RF scaling laws and suggest the possibility of accumulative effects influencing the field enhancement factor.

Structural Polymorphism in d(T).d(A)*d(T) Triple Helices

DNA triple helices containing two thymine strands and one adenine strand have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that the structure with a parallel orientation of the third strand, in which the third strand base forms Hoogsteen hydrogen bonds with the adenine base in the Watson-Crick duplex, is energetically the most favourable. An antiparallel orientation of the third strand is also possible, in which the third strand base hydrogen bonds to both the bases in the Watson-Crick duplex. This structure is energetically comparable to the parallel structure. For the parallel triplex a 200ps molecular dynamics simulation starting from two different starting structures indicates that at 300K significant structural heterogeneity exists in this tripler structure. The results are compared with existing structural data on this class of triplexes derived from theoretical and NMR techniques.

Effect of Sorbate-Zeolite Interaction on Cluster Lifetime and Size of Sorbates: Xe in NaY

Molecular dynamics calculations are reported for Xe in sodium Y zeolite with varying strengths of sorbate-zeolite dispersion interaction. In the absence of any dispersion interaction between the sorbate and the zeolite, the presence of the zeolite has a purely geometrical role. Increase in the strength of the sorbate-zeolite interaction increases the monomer population and decreases the population of dimers and higher sized clusters. The lifetime of the monomers as well as dimers increases with the strength of the dispersion interaction. The observed variations in the lifetime and the population of the different sized clusters is explained in terms of the changes in the potential energy surface caused by the increase in the strength of the dispersion interaction.

Influence of non-geometrical factors on intracrystalline diffusion -- Role of sorbate-zeolite interactions

Molecular dynamics simulations on Xe in NaY and Ar in NaCaA zeolite are reported. Rates of cage-to-cage crossovers in the two zeolites exhibit trends which are contrary to that expected from geometrical considerations. The results suggest the important role of the sorbate-zeolite interactions in determining the molecular sieve properties of zeolites for small sized sorbates. The results are explained in terms of the barrier height for cage-to-cage crossover in the two zeolites.

Nonlinear hydrodynamics of a hard-sphere fluid near the glass transition

We conduct a numerical study of the dynamic behavior of a dense hard-sphere fluid by deriving and integrating a set of Langevin equations. The statics of the system is described by a free-energy functional of the Ramakrishnan-Yussouff form. We find that the system exhibits glassy behavior as evidenced through a stretched exponential decay and a two-stage relaxation of the density correlation function. The characteristic times grow with increasing density according to the Vogel-Fulcher law. The wave-number dependence of the kinetics is extensively explored. The connection of our results with experiment, mode-coupling theory, and molecular-dynamics results is discussed.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations. (C) 2011 American Institute of Physics. doi:10.1063/1.3516588]

Recognition of Polycyclic Aromatic Hydrocarbons and Their Derivatives by the 1,3-Dinaphthalimide Conjugate of Calix4]arene: Emission, Absorption, Crystal Structures, and Computational Studies

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants as well as well-known carcinogens. Therefore, it is important to develop an effective receptor for the detection and quantification of such molecules in solution. In view of this, a 1,3-dinaphthalimide derivative of calix4]arene (L) has been synthesized and characterized, and the structure has been established by single crystal XRD. In the crystal lattice, intermolecular arm-to-arm pi center dot center dot center dot pi overlap dominates and thus L becomes a promising receptor for providing interactions with the aromatic species in solution, which can be monitored by following the changes that occur in its fluorescence and absorption spectra. On the basis of the solution studies carried out with about 17 derivatives of the aromatic guest molecular systems, it may be concluded that the changes that occur in the fluorescence intensity seem to be proportional to the number of aromatic rings present and thus proportional to the extent of pi center dot center dot center dot pi interaction present between the naphthalimide moieties and the aromatic portion of the guest molecule. Though the nonaromatic portion of the guest species affects the fluorescence quenching, the trend is still based on the number of rings present in these. Four guest aldehydes are bound to L with K-ass of 2000-6000 M-1 and their minimum detection limit is in the range of 8-35 mu M. The crystal structure of a naphthaldehyde complex, L.2b, exhibits intermolecular arm-to-arm as well as arm-to-naphthaldehyde pi center dot center dot center dot pi interactions. Molecular dynamics studies of L carried out in the presence of aromatic aldehydes under vacuum as well as in acetonitrile resulted in exhibiting interactions observed in the solid state and hence the changes observed in the fluorescence and absorption spectra are attributable for such interactions. Complex formation has also been delineated through ESI MS studies. Thus L is a promising receptor that can recognize PAHs by providing spectral changes proportional to the aromatic conjugation of the guest and the extent of aromatic pi center dot center dot center dot pi interactions present between L and the guest.

Diffusion of sorbates in zeolites Y and A novel dependence on sorbate size and strength of sor ba t e-Zeoli t e interaction

A systematic investigation of monatomic spherical sorbates in the supercages of zeolites Y and A by molecular dynamics technique is presented. Rates of intercage diffusion, rates of cage visits, and the diffusion coefficients have been calculated as a function of the sorbate-zeolite interaction strength. These properties exhibit markedly different dependences on interaction strength for the two zeolites. The observed behavior is shown to be a consequence of the two principal mechanisms of intercage diffusion and the energetic barrier associated with them. The diffusion coefficient and other properties associated with intercage diffusion are found to be directly proportional to the reciprocal of the square of the sorbate diameter when the sorbate diameter is significantly smaller than the window diameter. As the sorbate diameter increases, a peak is observed in all the transport properties investigated including the diffusion coefficient. We call this surprising effect as the ring or levitation effect and it explains several anomalous results reported in the literature and suggests a breakdown of the geometrical criterion for diffusion of sorbates. It shows that under certain conditions nongeometrical factors play a major role and geometrical factors become secondary in the determination of the molecular sieve property. A generalized parameter has been proposed which suggests conditions under which one can expect the ring or levitation effect in any porous medium. Inverse size selectivity becomes operative under these conditions.

Xenon in sodium Y zeolite. 2. Arrhenius relation, mechanism, and barrier height distribution for cage-to-cage diffusion

Various geometrical and energetic distribution functions and other properties connected with the cage-to-cage diffusion of xenon in sodium Y zeolite have been obtained from long molecular dynamics calculations. Analysis of diffusion pathways reveals two interesting mechanisms-surface-mediated and centralized modes for cage-to-cage diffusion. The surface-mediated mode of diffusion exhibits a small positive barrier, while the centralized diffusion exhibits a negative barrier for the sorbate to diffuse across the 12-ring window. In both modes, however, the sorbate has to be activated from the adsorption site to enable it to gain mobility. The centralized diffusion additionally requires the sorbate to be free of the influence of the surface of the cage as well. The overall rate for cage-to-cage diffusion shows an Arrhenius temperature dependence with E(a) = 3 kJ/mol. It is found that the decay in the dynamical correction factor occurs on a time scale comparable to the cage residence time. The distributions of barrier heights have been calculated. Functions reflecting the distribution of the sorbate-zeolite interaction at the window and the variations of the distance between the sorbate and the centers of the parent and daughter cages are presented.

Probing potential energy surfaces in confined systems: behavior of mean-square displacement in zeolites

Time evolution of mean-squared displacement based on molecular dynamics for a variety of adsorbate-zeolite systems is reported. Transition from ballistic to diffusive behavior is observed for all the systems. The transition times are found to be system dependent and show different types of dependence on temperature. Model calculations on a one-dimensional system are carried out which show that the characteristic length and transition times are dependent on the distance between the barriers, their heights, and temperature. In light of these findings, it is shown that it is possible to obtain valuable information about the average potential energy surface sampled under specific external conditions.

Inherent structures of phase-separating binary mixtures: Nucleation, spinodal decomposition, and pattern formation

An energy landscape view of phase separation and nonideality in binary mixtures is developed by exploring their potential energy landscape (PEL) as functions of temperature and composition. We employ molecular dynamics simulations to study a model that promotes structure breaking in the solute-solvent parent binary liquid, at low temperatures. The PEL of the system captures the potential energy distribution of the inherent structures (IS) of the system and is obtained by removing the kinetic energy (including that of intermolecular vibrations). The broader distribution of the inherent structure energy for structure breaking liquid than that of the structure making liquid demonstrates the larger role of entropy in stabilizing the parent liquid of the structure breaking type of binary mixtures. At high temperature, although the parent structure of the structure breaking binary mixture is homogenous, the corresponding inherent structure is found to be always phase separated, with a density pattern that exhibits marked correlation with the energy of its inherent structure. Over a broad range of intermediate inherent structure energy, bicontinuous phase separation prevails with interpenetrating stripes as signatures of spinodal decomposition. At low inherent structure energy, the structure is largely phase separated with one interface where as at high inherent structure energy we find nucleation type growth. Interestingly, at low temperature, the average inherent structure energy (< EIS >) exhibits a drop with temperature which signals the onset of crystallization in one of the phases while the other remains in the liquid state. The nonideal composition dependence of viscosity is anticorrelated with average inherent structure energy.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Interaction of single-walled carbon nanotubes with poly(propyl ether imine) dendrimers

We study the complexation of nontoxic, native poly(propyl ether imine) dendrimers with single-walled carbon nanotubes (SWNTs). The interaction was monitored by measuring the quenching of inherent fluorescence of the dendrimer. The dendrimer-nanotube binding also resulted in the increased electrical resistance of the hole doped SWNT, due to charge-transfer interaction between dendrimer and nanotube. This charge-transfer interaction was further corroborated by observing a shift in frequency of the tangential Raman modes of SWNT. We also report the effect of acidic and neutral pH conditions on the binding affinities. Experimental studies were supplemented by all atom molecular dynamics simulations to provide a microscopic picture of the dendrimer-nanotube complex. The complexation was achieved through charge transfer and hydrophobic interactions, aided by multitude of oxygen, nitrogen, and n-propyl moieties of the dendrimer. (C) 2011 American Institute of Physics. doi:10.1063/1.3561308]

Orientational relaxation in dipolar systems: How much do we understand the role of correlations

Dipolar systems, both liquids and solids, constitute a class of naturally abundant systems that are important in all branches of natural science. The study of orientational relaxation provides a powerful method to understand the microscopic properties of these systems and, fortunately, there are many experimental tools to study orientational relaxation in the condensed phases. However, even after many years of intense research, our understanding of orientational relaxation in dipolar systems has remained largely imperfect. A major hurdle towards achieving a comprehensive understanding is the long range and complex nature of dipolar interactions which also made reliable theoretical study extremely difficult. These difficulties have led to the development of continuum model based theories, which although they provide simple, elegant expressions for quantities of interest, are mostly unsatisfactory as they totally neglect the molecularity of inter-molecular interactions. The situation has improved in recent years because of renewed studies, led by computer simulations. In this review, we shall address some of the recent advances, with emphasis on the work done in our laboratory at Bangalore. The reasons for the failure of the continuum model, as revealed by the recent Brownian dynamics simulations of the dipolar lattice, are discussed. The main reason is that the continuum model predicts too fast a decay of the torque-torque correlation function. On the other hand, a perturbative calculation, based on Zwanzig's projection operator technique, provides a fairly satisfactory description of the single particle orientational dynamics for not too strongly polar dipolar systems. A recently developed molecular hydrodynamic theory that properly includes the effects of intermolecular orientational pair correlations provides an even better description of the single-particle orientational dynamics. We also discuss the rank dependence of the dielectric friction. The other topics reviewed here includes dielectric relaxation and solvation dynamics, as they are intimately connected with orientational relaxation. Recent molecular dynamics simulations of the dipolar lattice are also discussed. The main theme of the present review is to understand the effects of intermolecular interactions on orientational relaxation. The presence of strong orientational pair correlation leads to a strong coupling between the single particle and the collective dynamics. This coupling can lead to rich dynamical properties, some of which are detailed here, while a major part remains yet unexplored.