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

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

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

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

Monte Carlo Study of Short-Range Order and Displacement Effects in Disordered CuAu

The correlation between local chemical environment and atomic displacements in disordered CuAu alloy has been studied using Monte Carlo simulations based on the effective medium theory (EMT) of metallic cohesion. These simulations correctly reproduce the chemically-specific nearest-neighbor distances in the random alloy across the entire Cu\$_x\$Au\$_{1-x}\$ concentration range. In the random equiatomic CuAu alloy, the chemically specific pair distances depend strongly on the local atomic environment (i.e. fraction of like/unlike nearest neighbors). In CuAu alloy with short-range order, the relationship between local environment and displacements remains qualitatively similar. However the increase in short-range order causes the average Cu-Au distance to decrease below the average Cu-Cu distance, as it does in the ordered CuAuI phase. Many of these trends can be understood qualitatively from the different neutral sphere radii and compressibilities of the Cu and Au atoms.Comment: 9 pages, 5 figures, 2 table

Bayesian Error Estimation in Density Functional Theory

We present a practical scheme for performing error estimates for Density Functional Theory calculations. The approach which is based on ideas from Bayesian statistics involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities like binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.Comment: 5 pages, 3 figure

Computational Design of Chemical Nanosensors: Metal Doped Carbon Nanotubes

We use computational screening to systematically investigate the use of transition metal doped carbon nanotubes for chemical gas sensing. For a set of relevant target molecules (CO, NH3, H2S) and the main components of air (N2, O2, H2O), we calculate the binding energy and change in conductance upon adsorption on a metal atom occupying a vacancy of a (6,6) carbon nanotube. Based on these descriptors, we identify the most promising dopant candidates for detection of a given target molecule. From the fractional coverage of the metal sites in thermal equilibrium with air, we estimate the change in the nanotube resistance per doping site as a function of the target molecule concentration assuming charge transport in the diffusive regime. Our analysis points to Ni-doped nanotubes as candidates for CO sensors working under typical atmospheric conditions

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

Dislocation Kinks in Copper: Widths, Barriers, Effective Masses, and Quantum Tunneling

We calculate the widths, migration barriers, effective masses, and quantum tunneling rates of kinks and jogs in extended screw dislocations in copper, using an effective medium theory interatomic potential. The energy barriers and effective masses for moving a unit jog one lattice constant are close to typical atomic energies and masses: tunneling will be rare. The energy barriers and effective masses for the motion of kinks are unexpectedly small due to the spreading of the kinks over a large number of atoms. The effective masses of the kinks are so small that quantum fluctuations will be important. We discuss implications for quantum creep, kink--based tunneling centers, and Kondo resonances