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

Graphene on metals: a Van der Waals density functional study

We use density functional theory (DFT) with a recently developed van der Waals density functional (vdW-DF) to study the adsorption of graphene on Al, Cu, Ag, Au, Pt, Pd, Co and Ni(111) surfaces. In constrast to the local density approximation (LDA) which predicts relatively strong binding for Ni,Co and Pd, the vdW-DF predicts weak binding for all metals and metal-graphene distances in the range 3.40-3.72 \AA. At these distances the graphene bandstructure as calculated with DFT and the many-body G$_0$W$_0$ method is basically unaffected by the substrate, in particular there is no opening of a band gap at the $K$-point.Comment: 4 pages, 3 figure

Towards electron transport measurements in chemically modified graphene: The effect of a solvent

Chemical functionalization of graphene modifies the local electron density of the carbon atoms and hence electron transport. Measuring these changes allows for a closer understanding of the chemical interaction and the influence of functionalization on the graphene lattice. However, not only chemistry, in this case diazonium chemistry, has an effect on the electron transport. Latter is also influenced by defects and dopants resulting from different processing steps. Here, we show that solvents used in the chemical reaction process change the transport properties. In more detail, the investigated combination of isopropanol and heating treatment reduces the doping concentration and significantly increases the mobility of graphene. Furthermore, the isopropanol treatment alone increases the concentration of dopants and introduces an asymmetry between electron and hole transport which might be difficult to distinguish from the effect of functionalization. The results shown in this work demand a closer look on the influence of solvents used for chemical modification in order to understand their influence

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

Loop Model with Generalized Fugacity in Three Dimensions

A statistical model of loops on the three-dimensional lattice is proposed and is investigated. It is O(n)-type but has loop fugacity that depends on global three-dimensional shapes of loops in a particular fashion. It is shown that, despite this non-locality and the dimensionality, a layer-to-layer transfer matrix can be constructed as a product of local vertex weights for infinitely many points in the parameter space. Using this transfer matrix, the site entropy is estimated numerically in the fully packed limit.Comment: 16pages, 4 eps figures, (v2) typos and Table 3 corrected. Refs added, (v3) an error in an explanation of fig.2 corrected. Refs added. (v4) Changes in the presentatio

Construction of transferable spherically-averaged electron potentials

A new scheme for constructing approximate effective electron potentials within density-functional theory is proposed. The scheme consists of calculating the effective potential for a series of reference systems, and then using these potentials to construct the potential of a general system. To make contact to the reference system the neutral-sphere radius of each atom is used. The scheme can simplify calculations with partial wave methods in the atomic-sphere or muffin-tin approximation, since potential parameters can be precalculated and then for a general system obtained through simple interpolation formulas. We have applied the scheme to construct electron potentials of phonons, surfaces, and different crystal structures of silicon and aluminum atoms, and found excellent agreement with the self-consistent effective potential. By using an approximate total electron density obtained from a superposition of atom-based densities, the energy zero of the corresponding effective potential can be found and the energy shifts in the mean potential between inequivalent atoms can therefore be directly estimated. This approach is shown to work well for surfaces and phonons of silicon.Comment: 8 pages (3 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

Interatomic interactions in the effective-medium theory

An expression is derived for the total energy of a system of interacting atoms based on an ansatz for the total electron density of the system as a superposition of atom densities taken from calculations for the atoms embedded in a homogeneous electron gas. This leads to an expression for the interaction energy in terms of the embedding energy of the atoms in a homogeneous electron gas, and corrections accounting, for instance, for the d-d hybridization in the transition metals. The density of the homogeneous electron gas is chosen as the average of the density from the surrounding atoms. Due to the variational property of the total-energy functional, the errors in the interaction energy are second order in the deviation of the ansatz density from the true ground-state value. The applicability of the approach is illustrated by calculations of the cohesive properties of some simple metals and all the 3d transition metals. The interaction energy can be expressed in a form simple enough to allow calculations for low-symmetry systems and is very well suited for simulations of time-dependent and finite-temperature problems. Preliminary results for the phonon-dispersion relations and the surface energies and relaxations for Al are used to illustrate the versatility of the approach. The division of the total energy into a density-dependent part, an electrostatic ‘‘pair-potential’’ part, and a hybridization part provides a very simple way of understanding a number of these phenomena.Peer reviewe