Niels Grønbech-Jensen

Simulation of protein folding by reaction path annealing

We present a systematic application of reaction path sampling to computer simulations of the folding of peptides and small proteins at atomic resolution in the presence of solvent. We use a simulated annealing protocol to generate an ensemble of room temperature folding trajectories of fixed length, which connect predetermined initial and final states. The trajectories are distributed according to a discretized version of the Onsager–Machlup action functional. We show that, despite the enormous practical restrictions placed on the number of time slices which can be explored, some of the basic kinetic features found experimentally for the folding of peptides and small proteins are exhibited in the nature of the reaction paths sampled. We test the method on three systems: A 12 residue α-helical peptide, a 16 residue β-hairpin peptide, and the 36 residue avian Pancreatic Polypeptide (aPP). All systems are represented at atomic resolution, and include explicit water molecules. For the 12 residue α-helix, we f...

First-principles study of luminescence in Ce-doped inorganic scintillators

Luminescence in Ce doped materials corresponds to a transition from an excited state where the lowest Ce 5d level is filled to the ground state where a single 4f level is filled. We have performed theoretical calculations based on Density Functional Theory to calculate the ground state band structure of Ce-doped materials as well as the Ce3+ excited state. The excited state calculations used a constrained occupancy approach by setting the occupation of the Ce 4f states to zero and allowing the first excited state above them to be filled. These calculations were performed on a set of Ce doped materials that are known from experiment to be scintillators or non-scintillators to relate theoretically calculable parameters to measured scintillator performance. From these studies we developed a set of criteria based on calculated parameters that are necessary characteristics for bright Ce activated scintillators. Applying these criteria to about a hundred new materials we developed a list of candidate materials for new bright Ce activated scintillators. After synthesis in powder form one of these new materials (Ba2YCl7:Ce) was found to be a bright scintillator. This approach, involving first-principles calculations of modest computing requirements was designed as a systematic, high-throughput method to aid in the discovery of new bright scintillator materials by prioritization and down-selection on the large number of potential new materials.

Determination of the headgroup-gold(111) potential surface for alkanethiol self-assembled monolayers by ab initio calculation

Abstract We present a realistic empirical potential function to model the head-group interaction for self-assembled monolayers (SAMs) of alkanethiols on Au(111). The potential function is fit to data obtained by ab initio geometry optimization of SCH 3 on Au(111) clusters. The principal result from our calculations is that barriers within the surface corrugation potential are too small to pin S atoms at any particular site. We note that simulations of alkanethiol/gold systems that employ a model precluding lateral movement of S cannot reproduce all dynamical behavior of the SAM.

A simple and effective Verlet-type algorithm for simulating Langevin dynamics

We present a revision to the well known Störmer–Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behaviour of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency and time step for both underdamped and overdamped behaviour within the usual stability limit of the Verlet algorithm. Given the structure and simplicity of the method, we conclude that this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints.

HALL NOISE AND TRANSVERSE FREEZING IN DRIVEN VORTEX LATTICES

We study driven vortex lattices in superconducting thin films. Above the critical force F{sub c} we find two dynamical phase transitions at F{sub p} and F{sub t} , which could be observed in simultaneous noise measurements of the longitudinal and Hall voltage. At F{sub p} there is a transition from plastic flow to smectic flow, where the voltage noise is isotropic (Hall noise = longitudinal noise) and there is a peak in the differential resistance. At F{sub t} there is a sharp transition to a frozen transverse solid, where the Hall noise falls abruptly and vortex motion is localized in the transverse direction. {copyright} {ital 1999} {ital The American Physical Society}

Efficient molecular dynamics scheme for the calculation of dopant profiles due to ion implantation

We present a highly efficient molecular dynamics scheme for calculating the concentration depth profile of dopants in ion irradiated materials. The scheme incorporates several methods for reducing the computational overhead, plus a rare event algorithm that allows statistically reliable results to be obtained over a range of several orders of magnitude in the dopant concentration. We give examples of using this scheme for calculating concentration profiles of dopants in crystalline silicon. Here we can predict the experimental profile over five orders of magnitude for both channeling and nonchanneling implants at energies up to hundreds of keV. The scheme has advantages over binary collision approximation (BCA) simulations, in that it does not rely on a large set of empirically fitted parameters. Although our scheme has a greater computational overhead than the BCA, it is far superior in the low ion energy regime, where the BCA scheme becomes invalid.

Interactions between charged spheres in divalent counterion solution

We simulate model systems of charged spherical particles in their counterion solution and measure the thermodynamic pressure and the pair distribution function from which we derive effective potentials of mean force. For a system with only electrostatic and hard core interactions, we investigate the effective potential between two like-charged spheres in divalent counterion solution as a function of concentration. We find a strong attractive interaction for high concentration and a global repulsive effective interaction for dilute systems. The results indicate a first order phase transition in sphere–counterion density as a function of global concentration and the effective sphere–sphere potentials in the dilute (solvated) regime suggest significant density fluctuations due to short range local minima in the effective energy surface. Our results arise from a minimal approach model of several recent experiments on polystyrene latex particles in monovalent counterion solution.

50 GFlops molecular dynamics on the Connection Machine-5

The authors present timings and performances numbers for a new short range three dimensional (3-D) molecular dynamics (MD) code, SPaSM, on the Connection Machine-5 (CM-5). They demonstrate that runs with more than 10/sup 8/ particles are now possible on massively parallel MIMD computers. To the best of their knowledge this is at least an order of magnitude more particles than what was previously been reported. Typical production runs show sustained performance (including communication) in the range of 47-50 GFlops on a 1024 node CM-5 with vector units (VUs). The speed of the code scales linearly with the number of processors and with the number of particles and shows 95% parallel efficiency in the speedup.

Lekner summation of Coulomb interactions in partially periodic systems

We present Lekner summations of long-range interactions in three-dimensional media, which are periodic in one or two dimensions. While the basic summation techniques are well known from Lekners original work, we emhasize a simple method for correctly evaluating the selfenergies of particles in a partially periodic lattice.

Complex dynamical flow phases and pinning in superconductors with rectangular pinning arrays

We examine vortex pinning and dynamics in thin-film superconductors interacting with square and rectangular pinning arrays for varied vortex densities including densities significantly larger than the pinning density. For both square and rectangular pinning arrays, the critical depinning force shows maxima at only certain integer matching fields where the vortices can form highly ordered arrays. For rectangular arrays the depinning force and commensurability effects are anisotropic with a much lower depinning threshold for vortex motion in the easy flow directions. We find evidence for a crossover in pinning behavior in rectangular pinning arrays as the field is increased. We also show analytically, and confirm with simulations, that for