Unbiased sampling of globular lattice proteins in three dimensions

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system

A tree-decomposed transfer matrix for computing exact Potts model partition functions for arbitrary graphs, with applications to planar graph colourings

Combining tree decomposition and transfer matrix techniques provides a very general algorithm for computing exact partition functions of statistical models defined on arbitrary graphs. The algorithm is particularly efficient in the case of planar graphs. We illustrate it by computing the Potts model partition functions and chromatic polynomials (the number of proper vertex colourings using Q colours) for large samples of random planar graphs with up to N=100 vertices. In the latter case, our algorithm yields a sub-exponential average running time of ~ exp(1.516 sqrt(N)), a substantial improvement over the exponential running time ~ exp(0.245 N) provided by the hitherto best known algorithm. We study the statistics of chromatic roots of random planar graphs in some detail, comparing the findings with results for finite pieces of a regular lattice.Comment: 5 pages, 3 figures. Version 2 has been substantially expanded. Version 3 shows that the worst-case running time is sub-exponential in the number of vertice

Rate theory for correlated processes: Double-jumps in adatom diffusion

We study the rate of activated motion over multiple barriers, in particular the correlated double-jump of an adatom diffusing on a missing-row reconstructed Platinum (110) surface. We develop a Transition Path Theory, showing that the activation energy is given by the minimum-energy trajectory which succeeds in the double-jump. We explicitly calculate this trajectory within an effective-medium molecular dynamics simulation. A cusp in the acceptance region leads to a sqrt{T} prefactor for the activated rate of double-jumps. Theory and numerical results agree

Performance evaluation of an emergency call center: tropical polynomial systems applied to timed Petri nets

We analyze a timed Petri net model of an emergency call center which processes calls with different levels of priority. The counter variables of the Petri net represent the cumulated number of events as a function of time. We show that these variables are determined by a piecewise linear dynamical system. We also prove that computing the stationary regimes of the associated fluid dynamics reduces to solving a polynomial system over a tropical (min-plus) semifield of germs. This leads to explicit formul{\ae} expressing the throughput of the fluid system as a piecewise linear function of the resources, revealing the existence of different congestion phases. Numerical experiments show that the analysis of the fluid dynamics yields a good approximation of the real throughput.Comment: 21 pages, 4 figures. A shorter version can be found in the proceedings of the conference FORMATS 201

Finite average lengths in critical loop models

A relation between the average length of loops and their free energy is obtained for a variety of O(n)-type models on two-dimensional lattices, by extending to finite temperatures a calculation due to Kast. We show that the (number) averaged loop length L stays finite for all non-zero fugacities n, and in particular it does not diverge upon entering the critical regime n -> 2+. Fully packed loop (FPL) models with n=2 seem to obey the simple relation L = 3 L_min, where L_min is the smallest loop length allowed by the underlying lattice. We demonstrate this analytically for the FPL model on the honeycomb lattice and for the 4-state Potts model on the square lattice, and based on numerical estimates obtained from a transfer matrix method we conjecture that this is also true for the two-flavour FPL model on the square lattice. We present in addition numerical results for the average loop length on the three critical branches (compact, dense and dilute) of the O(n) model on the honeycomb lattice, and discuss the limit n -> 0. Contact is made with the predictions for the distribution of loop lengths obtained by conformal invariance methods.Comment: 20 pages of LaTeX including 3 figure

Unraveling the acoustic electron-phonon interaction in graphene

Using a first-principles approach we calculate the acoustic electron-phonon couplings in graphene for the transverse (TA) and longitudinal (LA) acoustic phonons. Analytic forms of the coupling matrix elements valid in the long-wavelength limit are found to give an almost quantitative description of the first-principles based matrix elements even at shorter wavelengths. Using the analytic forms of the coupling matrix elements, we study the acoustic phonon-limited carrier mobility for temperatures 0-200 K and high carrier densities of 10^{12}-10^{13} cm^{-2}. We find that the intrinsic effective acoustic deformation potential of graphene is \Xi_eff = 6.8 eV and that the temperature dependence of the mobility \mu ~ T^{-\alpha} increases beyond an \alpha = 4 dependence even in the absence of screening when the full coupling matrix elements are considered. The large disagreement between our calculated deformation potential and those extracted from experimental measurements (18-29 eV) indicates that additional or modified acoustic phonon-scattering mechanisms are at play in experimental situations.Comment: 7 pages, 3 figure

Exact enumeration of Hamiltonian circuits, walks, and chains in two and three dimensions

We present an algorithm for enumerating exactly the number of Hamiltonian chains on regular lattices in low dimensions. By definition, these are sets of k disjoint paths whose union visits each lattice vertex exactly once. The well-known Hamiltonian circuits and walks appear as the special cases k=0 and k=1 respectively. In two dimensions, we enumerate chains on L x L square lattices up to L=12, walks up to L=17, and circuits up to L=20. Some results for three dimensions are also given. Using our data we extract several quantities of physical interest

Dense loops, supersymmetry, and Goldstone phases in two dimensions

Loop models in two dimensions can be related to O(N) models. The low-temperature dense-loops phase of such a model, or of its reformulation using a supergroup as symmetry, can have a Goldstone broken-symmetry phase for N<2. We argue that this phase is generic for -2< N <2 when crossings of loops are allowed, and distinct from the model of non-crossing dense loops first studied by Nienhuis [Phys. Rev. Lett. 49, 1062 (1982)]. Our arguments are supported by our numerical results, and by a lattice model solved exactly by Martins et al. [Phys. Rev. Lett. 81, 504 (1998)].Comment: RevTeX, 5 pages, 3 postscript figure

Simulations of energetic beam deposition: from picoseconds to seconds

We present a new method for simulating crystal growth by energetic beam deposition. The method combines a Kinetic Monte-Carlo simulation for the thermal surface diffusion with a small scale molecular dynamics simulation of every single deposition event. We have implemented the method using the effective medium theory as a model potential for the atomic interactions, and present simulations for Ag/Ag(111) and Pt/Pt(111) for incoming energies up to 35 eV. The method is capable of following the growth of several monolayers at realistic growth rates of 1 monolayer per second, correctly accounting for both energy-induced atomic mobility and thermal surface diffusion. We find that the energy influences island and step densities and can induce layer-by-layer growth. We find an optimal energy for layer-by-layer growth (25 eV for Ag), which correlates with where the net impact-induced downward interlayer transport is at a maximum. A high step density is needed for energy induced layer-by-layer growth, hence the effect dies away at increased temperatures, where thermal surface diffusion reduces the step density. As part of the development of the method, we present molecular dynamics simulations of single atom-surface collisions on flat parts of the surface and near straight steps, we identify microscopic mechanisms by which the energy influences the growth, and we discuss the nature of the energy-induced atomic mobility