Evaluation of Constant Potential Method in Simulating Electric Double-Layer Capacitors

A major challenge in the molecular simulation of electric double layer capacitors (EDLCs) is the choice of an appropriate model for the electrode. Typically, in such simulations the electrode surface is modeled using a uniform fixed charge on each of the electrode atoms, which ignores the electrode response to local charge fluctuations induced by charge fluctuations in the electrolyte. In this work, we evaluate and compare this Fixed Charge Method (FCM) with the more realistic Constant Potential Method (CPM), [Reed, et al., J. Chem. Phys., 126, 084704 (2007)], in which the electrode charges fluctuate in order to maintain constant electric potential in each electrode. For this comparison, we utilize a simplified LiClO$_4$-acetonitrile/graphite EDLC. At low potential difference ($\Delta\Psi\le 2V$), the two methods yield essentially identical results for ion and solvent density profiles; however, significant differences appear at higher $\Delta\Psi$. At $\Delta\Psi\ge 4V$, the CPM ion density profiles show significant enhancement (over FCM) of "partially electrode solvated" Li$^+$ ions very close to the electrode surface. The ability of the CPM electrode to respond to local charge fluctuations in the electrolyte is seen to significantly lower the energy (and barrier) for the approach of Li$^+$ ions to the electrode surface.Comment: Corrected typo

A molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferro-solids the observed susceptibility is considerably lowered when compared to ferrofluids.Comment: 33 pages including 12 figures, requires RevTex

Model Channel Ion Currents in NaCl - SPC/E Solution with Applied-Field Molecular Dynamics

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125 Angstrom internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and SPC/E water. Channel and bath currents were computed from ten 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration-dependent and superlinear at high concentrations.Comment: Accepted for publication in Biophysical Journa

Compressive auto-indexing in femtosecond nanocrystallography

Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells on the side. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a three dimensional (3D) diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques. "Indexing" algorithms used in crystallography enable orientation determination of diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show that it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.Comment: Spence Festschrift on Ultramicroscop

Amorphous silica between confining walls and under shear: a computer simulation study

Molecular dynamics computer simulations are used to investigate a silica melt confined between walls at equilibrium and in a steady-state Poisseuille flow. The walls consist of point particles forming a rigid face-centered cubic lattice and the interaction of the walls with the melt atoms is modelled such that the wall particles have only a weak bonding to those in the melt, i.e. much weaker than the covalent bonding of a Si-O unit. We observe a pronounced layering of the melt near the walls. This layering, as seen in the total density profile, has a very irregular character which can be attributed to a preferred orientational ordering of SiO4 tetrahedra near the wall. On intermediate length scales, the structure of the melt at the walls can be well distinguished from that of the bulk by means of the ring size distribution. Whereas essentially no structural changes occur in the bulk under the influence of the shear fields considered, strong structural rearrangements in the ring size distribution are present at the walls as far as there is a slip motion. For the sheared system, parabolic velocity profiles are found in the bulk region as expected from hydrodynamics and the values for the shear viscosity as extracted from those profiles are in good agreement with those obtained in pure bulk simulations from the appropriate Green-Kubo formula.Comment: 23 pages of Late

Strongly Charged, Flexible Polyelectrolytes in Poor Solvents -- Molecular Dynamics Simulations

We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By varying the polymer density and the electrostatic interaction strength we study the crossover from a dominating electrostatic interaction to the regime of strong screening, where the hydrophobic interactions dominate. During the crossover a multitude of structures is observed. In the limit of low polymer density strongly stretched, necklace like conformations are found. In the opposite limit of high polymer density which is equivalent to strongly screened electrostatic interactions, we find that the chains are extremely collapsed, however we observe no agglomeration or phase separation. The investigations show that the density of free charges is one of the relevant parameters which rules the behavior of the system and hence should be used as a parameter to explain experimental results.Comment: 42 pages, including 22 figures and 2 table

Ewald methods for inverse power-law interactions in tridimensional and quasi-two dimensional systems

In this paper, we derive the Ewald method for inverse power-law interactions in quasi-two dimensional systems. The derivation is done by using two different analytical methods. The first uses the Parry's limit, that considers the Ewald methods for quasi-two dimensional systems as a limit of the Ewald methods for tridimensional systems, the second uses Poisson-Jacobi identities for lattice sums. Taking into account the equivalence of both derivations, we obtain a new analytical Fourier transform intregral involving incomplete gamma function. Energies of the generalized restrictive primitive model of electrolytes ($\eta$-RPM) and of the generalized one component plasma model ($\eta$-OCP) are given for the tridimensional, quasi-two dimensional and monolayers systems. Few numerical results, using Monte-Carlo simulations, for $\eta$-RPM and $\eta$-OCP monolayers systems are reported.Comment: to be published in Journal of Physics A: Mathematical and Theoretical (19 pages, 2 figures and 3 tables