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

Extended two-level quantum dissipative system from bosonization of the elliptic spin-1/2 Kondo model

We study the elliptic spin-1/2 Kondo model (spin-1/2 fermions in one dimension with fully anisotropic contact interactions with a magnetic impurity) in the light of mappings to bosonic systems using the fermion-boson correspondence and associated unitary transformations. We show that for fixed fermion number, the bosonic system describes a two-level quantum dissipative system with two noninteracting copies of infinitely-degenerate upper and lower levels. In addition to the standard tunnelling transitions, and the transitions driven by the dissipative coupling, there are also bath-mediated transitions between the upper and lower states which simultaneously effect shifts in the horizontal degeneracy label. We speculate that these systems could provide new examples of continuous time quantum random walks, which are exactly solvable.Comment: 7 pages, 1 figur

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

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

Critical properties of joint spin and Fortuin-Kasteleyn observables in the two-dimensional Potts model

The two-dimensional Potts model can be studied either in terms of the original Q-component spins, or in the geometrical reformulation via Fortuin-Kasteleyn (FK) clusters. While the FK representation makes sense for arbitrary real values of Q by construction, it was only shown very recently that the spin representation can be promoted to the same level of generality. In this paper we show how to define the Potts model in terms of observables that simultaneously keep track of the spin and FK degrees of freedom. This is first done algebraically in terms of a transfer matrix that couples three different representations of a partition algebra. Using this, one can study correlation functions involving any given number of propagating spin clusters with prescribed colours, each of which contains any given number of distinct FK clusters. For 0 <= Q <= 4 the corresponding critical exponents are all of the Kac form h_{r,s}, with integer indices r,s that we determine exactly both in the bulk and in the boundary versions of the problem. In particular, we find that the set of points where an FK cluster touches the hull of its surrounding spin cluster has fractal dimension d_{2,1} = 2 - 2 h_{2,1}. If one constrains this set to points where the neighbouring spin cluster extends to infinity, we show that the dimension becomes d_{1,3} = 2 - 2 h_{1,3}. Our results are supported by extensive transfer matrix and Monte Carlo computations.Comment: 15 pages, 3 figures, 2 table

Tracking Data Acquisition System (TDAS) for the 1990's. Volume 6: TDAS navigation system architecture

One-way range and Doppler methods for providing user orbit and time determination are examined. Forward link beacon tracking, with on-board processing of independent navigation signals broadcast continuously by TDAS spacecraft; forward link scheduled tracking; with on-board processing of navigation data received during scheduled TDAS forward link service intervals; and return link scheduled tracking; with ground-based processing of user generated navigation data during scheduled TDAS return link service intervals are discussed. A system level definition and requirements assessment for each alternative, an evaluation of potential navigation performance and comparison with TDAS mission model requirements is included. TDAS satellite tracking is also addressed for two alternatives: BRTS and VLBI tracking

Dynamic rotor mode in antiferromagnetic nanoparticles

We present experimental, numerical, and theoretical evidence for a new mode of antiferromagnetic dynamics in nanoparticles. Elastic neutron scattering experiments on 8 nm particles of hematite display a loss of diffraction intensity with temperature, the intensity vanishing around 150 K. However, the signal from inelastic neutron scattering remains above that temperature, indicating a magnetic system in constant motion. In addition, the precession frequency of the inelastic magnetic signal shows an increase above 100 K. Numerical Langevin simulations of spin dynamics reproduce all measured neutron data and reveal that thermally activated spin canting gives rise to a new type of coherent magnetic precession mode. This "rotor" mode can be seen as a high-temperature version of superparamagnetism and is driven by exchange interactions between the two magnetic sublattices. The frequency of the rotor mode behaves in fair agreement with a simple analytical model, based on a high temperature approximation of the generally accepted Hamiltonian of the system. The extracted model parameters, as the magnetic interaction and the axial anisotropy, are in excellent agreement with results from Mossbauer spectroscopy

Critical exponents of domain walls in the two-dimensional Potts model

We address the geometrical critical behavior of the two-dimensional Q-state Potts model in terms of the spin clusters (i.e., connected domains where the spin takes a constant value). These clusters are different from the usual Fortuin-Kasteleyn clusters, and are separated by domain walls that can cross and branch. We develop a transfer matrix technique enabling the formulation and numerical study of spin clusters even when Q is not an integer. We further identify geometrically the crossing events which give rise to conformal correlation functions. This leads to an infinite series of fundamental critical exponents h_{l_1-l_2,2 l_1}, valid for 0 </- Q </- 4, that describe the insertion of l_1 thin and l_2 thick domain walls.Comment: 5 pages, 3 figures, 1 tabl

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

Phase diagram and critical exponents of a Potts gauge glass

The two-dimensional q-state Potts model is subjected to a Z_q symmetric disorder that allows for the existence of a Nishimori line. At q=2, this model coincides with the +/- J random-bond Ising model. For q>2, apart from the usual pure and zero-temperature fixed points, the ferro/paramagnetic phase boundary is controlled by two critical fixed points: a weak disorder point, whose universality class is that of the ferromagnetic bond-disordered Potts model, and a strong disorder point which generalizes the usual Nishimori point. We numerically study the case q=3, tracing out the phase diagram and precisely determining the critical exponents. The universality class of the Nishimori point is inconsistent with percolation on Potts clusters.Comment: Latex, 7 pages, 3 figures, v2: 1 reference adde