Understanding the nucleation mechanisms of Carbon Nanotubes in catalytic Chemical Vapor Deposition

The nucleation of carbon caps on small nickel clusters is studied using a tight binding model coupled to grand canonical Monte Carlo simulations. It takes place in a well defined carbon chemical potential range, when a critical concentration of surface carbon atoms is reached. The solubility of carbon in the outermost Ni layers, that depends on the initial, crystalline or disordered, state of the catalyst and on the thermodynamic conditions, is therefore a key quantity to control the nucleation

Estimating statistical distributions using an integral identity

We present an identity for an unbiased estimate of a general statistical distribution. The identity computes the distribution density from dividing a histogram sum over a local window by a correction factor from a mean-force integral, and the mean force can be evaluated as a configuration average. We show that the optimal window size is roughly the inverse of the local mean-force fluctuation. The new identity offers a more robust and precise estimate than a previous one by Adib and Jarzynski [J. Chem. Phys. 122, 014114, (2005)]. It also allows a straightforward generalization to an arbitrary ensemble and a joint distribution of multiple variables. Particularly we derive a mean-force enhanced version of the weighted histogram analysis method (WHAM). The method can be used to improve distributions computed from molecular simulations. We illustrate the use in computing a potential energy distribution, a volume distribution in a constant-pressure ensemble, a radial distribution function and a joint distribution of amino acid backbone dihedral angles.Comment: 45 pages, 7 figures, simplified derivation, a more general mean-force formula, add discussions to the window size, add extensions to WHAM, and 2d distribution

Langlands duality for finite-dimensional representations of quantum affine algebras

We describe a correspondence (or duality) between the q-characters of finite-dimensional representations of a quantum affine algebra and its Langlands dual in the spirit of q-alg/9708006 and 0809.4453. We prove this duality for the Kirillov-Reshetikhin modules and their irreducible tensor products. In the course of the proof we introduce and construct "interpolating (q,t)-characters" depending on two parameters which interpolate between the q-characters of a quantum affine algebra and its Langlands dual.Comment: 40 pages; several results and comments added. Accepted for publication in Letters in Mathematical Physic

Enhancement of kinetic energy fluctuations due to expansion

Global equilibrium fragmentation inside a freeze out constraining volume is a working hypothesis widely used in nuclear fragmentation statistical models. In the framework of classical Lennard Jones molecular dynamics, we study how the relaxation of the fixed volume constraint affects the posterior evolution of microscopic correlations, and how a non-confined fragmentation scenario is established. A study of the dynamical evolution of the relative kinetic energy fluctuations was also performed. We found that asymptotic measurements of such observable can be related to the number of decaying channels available to the system at fragmentation time.Comment: 6 pages, 4 figure

Structure and thermodynamics of platelet dispersions

Various properties of fluids consisting of platelike particles differ from the corresponding ones of fluids consisting of spherical particles because interactions between platelets depend on their mutual orientations. One of the main issues in this topic is to understand how structural properties of such fluids depend on factors such as the shape of the platelets, the size polydispersity, the orientational order, and the platelet number density. A statistical mechanics approach to the problem is natural and in the last few years there has been a lot of work on the study of properties of platelet fluids. In this contribution some recent theoretical developments in the field are discussed and experimental investigations are described.Comment: 23 pages, 18 figure

WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectories

WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt with quantum dynamics of closed and open systems, respectively, the present Part III adds fully classical and mixed quantum-classical propagations to WavePacket. In those simulations classical phase-space densities are sampled by trajectories which follow (diabatic or adiabatic) potential energy surfaces. In the vicinity of (genuine or avoided) intersections of those surfaces trajectories may switch between surfaces. To model these transitions, two classes of stochastic algorithms have been implemented: (1) J. C. Tully's fewest switches surface hopping and (2) Landau-Zener based single switch surface hopping. The latter one offers the advantage of being based on adiabatic energy gaps only, thus not requiring non-adiabatic coupling information any more. The present work describes the MATLAB version of WavePacket 6.0.2 which is essentially an object-oriented rewrite of previous versions, allowing to perform fully classical, quantum-classical and quantum-mechanical simulations on an equal footing, i.e., for the same physical system described by the same WavePacket input. The software package is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics are available

Geometrical Frustration: A Study of 4d Hard Spheres

The smallest maximum kissing-number Voronoi polyhedron of 3d spheres is the icosahedron and the tetrahedron is the smallest volume that can show up in Delaunay tessalation. No periodic lattice is consistent with either and hence these dense packings are geometrically frustrated. Because icosahedra can be assembled from almost perfect tetrahedra, the terms "icosahedral" and "polytetrahedral" packing are often used interchangeably, which leaves the true origin of geometric frustration unclear. Here we report a computational study of freezing of 4d hard spheres, where the densest Voronoi cluster is compatible with the symmetry of the densest crystal, while polytetrahedral order is not. We observe that, under otherwise comparable conditions, crystal nucleation in 4d is less facile than in 3d. This suggest that it is the geometrical frustration of polytetrahedral structures that inhibits crystallization.Comment: 4 pages, 3 figures; revised interpretatio

A general theory of DNA-mediated and other valence-limited interactions

We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the configurational and combinatorial entropic factors that play a key role in valence-limited interactions. By rigorously enforcing self-consistency, it achieves near-quantitative accuracy with respect to detailed Monte Carlo calculations. With suitable approximations and in particular geometries, our theory reduces to previous successful treatments, which are now united in a common and extensible framework. We expect our tools to be useful to other researchers investigating ligand-mediated interactions. A complete and well-documented Python implementation is freely available at http://github.com/patvarilly/DNACC .Comment: 18 pages, 10 figure

Phase behavior of the Lattice Restricted Primitive Model with nearest-neighbor exclusion

The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to charge-ordered solid transition that terminates at the maximum density, $\rho^*_{max}=\sqrt2$ and reduced temperature $T^*\approx0.29$. At that point, there is a first-order phase transition between two phases of the same density, one charge-ordered and the other charge-disordered. The liquid-vapor transition for the model is metastable, lying entirely within the fluid-solid phase envelope.Comment: 6 pages, color. submitted to J. Chem. Phy

Off-lattice Monte Carlo Simulation of Supramolecular Polymer Architectures

We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational changes that exactly preserve fixed-length constraints of all bonds. The algorithm reproduces known end-to-end distance distributions for simple, analytically tractable systems of cross-linked stiff and freely jointed polymers flawlessly, and is used to determine the effective persistence length of short bundles of semi-flexible worm-like chains, cross-linked to each other. It reveals a possible regulatory mechanism in bundled networks: the effective persistence of bundles is controlled by the linker density.Comment: 4 pages, 4 figure