Determining the efficiency of a broad-energy HPGe detector using Monte Carlo simulations

Broad-energy HPGe detectors have a useful range of 3 keV to 3 MeV, making them ideal for the assay of environmental samples. Such measurements however, are hindered by variations in the sample matrix, summing effects, and the Compton continuum. Detectors may be characterised by proprietary software in such a situation, however Monte-Carlo modelling is a useful, inexpensive alternative that also provides greater flexibility when determining the detector response and efficiency during a measurement. In the current work, a full GEANT4 model of a broad-energy HPGe detector is presented, and simulations of various samples are compared to experimental data. These are found to be accurate within 3 % at a confidence level of 95 % for energies from 30 to 3,000 keV, with greater variations below 100 keV due to an increased sensitivity to geometrical inaccuracies.     

Characterisation of cascade summing effects in gamma spectroscopy using Monte Carlo simulations

A GEANT4 based Monte Carlo simulation has been successfully utilised to calculate peak efficiency characterisations and cascade summing (true coincidence summing) corrections in two source geometries commonly used for environmental monitoring. The cascade summing corrections are compared with values generated using an existing (validated) system, and found to be in excellent agreement for all radionuclides simulated. The calculated correction factors and peak efficiencies were also tested by analysing well defined sources used in the operation of the International Monitoring System, which undertakes radionuclide monitoring for verification of the Comprehensive Nuclear-Test-Ban Treaty. All abundances of the radionuclides measured matched the values that were previously determined using proprietary software. Using GEANT4 in this way, cascade summing corrections can now be extended to complex detector models and source matrices, such as Compton Suppression systems.     

Monte Carlo characterisation of a Compton suppressed broad-energy HPGe detector

GEANT4 Monte Carlo simulations have been successfully utilised to characterise a Compton suppressed broad-energy HPGe detector. The detector setup has been fully recreated in the simulation, which has been optimised to consistently reproduce the detector response. The peak efficiencies for both the primary BEGe detector and NaI(Tl) guard detectors agree with the simulated values for multiple test sources within 3 %. Compton suppression has also been simulated, with good agreement seen between the simulated and actual CSF values (<10 %) for multiple radionuclides. A secondary reference source was also simulated, which contained up to 30 radionuclides in a different geometry to that of the previous source. This showed excellent agreement with experimental data in both unsuppressed and suppressed modes of operation.     

Surface tension of associating fluids by Monte Carlo simulations

Canonical Monte Carlo (NVT-MC) simulations were performed to obtain surface tension and coexistence densities at the liquid-vapor interface of one-site associating Lennard-Jones and hard-core Yukawa fluids, as functions of association strength and temperature. The method to obtain the components of the pressure tensor from NVT-MC simulations was validated by comparing the equation of state of the associative hard sphere system with that coming from isothermal-isobaric Monte Carlo simulations. Surface tension of the associative Lennard-Jones fluid determined from NVT-MC is compared with previously reported results obtained by molecular dynamics simulations of a pseudomixture model of monomers and dimers. A good agreement was found between both methods. Values of surface tension of associative hard-core Yukawa fluids are presented here for the first time.     

Parallel Markov chain Monte Carlo simulations

With strict detailed balance, parallel Monte Carlo simulation through domain decomposition cannot be validated with conventional Markov chain theory, which describes an intrinsically serial stochastic process. In this work, the parallel version of Markov chain theory and its role in accelerating Monte Carlo simulations via cluster computing is explored. It is shown that sequential updating is the key to improving efficiency in parallel simulations through domain decomposition. A parallel scheme is proposed to reduce interprocessor communication or synchronization, which slows down parallel simulation with increasing number of processors. Parallel simulation results for the two-dimensional lattice gas model show substantial reduction of simulation time for systems of moderate and large size.     

Predicting helical hairpins from sequences by Monte Carlo simulations

The key problem in polypeptide‐structure prediction is with regard to thermodynamics. Two factors limit prediction in ab initio computer simulations. First, the thermodynamically dominant conformations must be found from an extremely large number of possible conformations. Second, these low‐energy forms must deviate little from the experimental structures. Here, we report on the application of the diffusion‐controlled Monte Carlo approach to predict four α‐helical hairpins with 34–38 residues by global optimization, using an energy optimized on other supersecondary structures. A total of seven simulations is carried out for each protein starting from fully extended conformations. Three proteins are correctly folded (within 3.0 Å rms from the experimental structures), but the fourth protein cannot distinguish between several equienergetic conformations. Possible improvement of the energy model is suggested. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 582–589, 2000     

Monte Carlo simulations of low background detectors

An implementation of the Electron Gamma Shower 4 code (EGS4) has been developed to allow convenient simulation of typical gamma ray measurement systems. Coincidence gamma rays, beta spectra, and angular correlations have been added to adequately simulate a complete nuclear decay and provide corrections to experimentally determined detector efficiencies. This code has been used to strip certain low-background spectra for the purpose of extremely low-level assay. Monte Carlo calculations of this sort can be extremely successful since low background detectors are usually free of significant contributions from poorly localized radiation sources, such as cosmic muons, secondary cosmic neutrons, and radioactive construction or shielding materials. Previously, validation of this code has been obtained from a series of comparisons between measurements and blind calculations. An example of the application of this code to an exceedingly low background spectrum stripping will be presented.Pacific Northwest Laboratory is operated by Battelle Memorial Institute for the US Department of Energy under Contract DE-AC06-76RLO 1830.     

Dynamic Monte Carlo simulations of anisotropic colloids

We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known. This approach - discarding hydrodynamics interactions - first allows us to improve the efficiency of previous dynamic Monte Carlo algorithms for spherical Brownian particles. In the second step, we address the case of anisotropic colloids with orientational degrees of freedom. As an illustration, we present a detailed study of the dynamics of thin platelets, with emphasis on long-time diffusion and orientational correlations.     

Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system

The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.     

Extensional flow of bulk polymers studied by dynamic Monte Carlo simulations

Dynamic Monte Carlo simulations of bulk lattice polymers driven through planar geometries with sequentially converging,parallel and diverging spaces between two neutrally repulsive solid plates are reported.The spatial profiles of polymer velocity and deformation along the course of such a laminar extensional flow have been carefully analyzed.The results appear consistent with experimental observations in literature.In the entrance and exit regions,a linear dependence of chain extension upon the excess velocity has been observed.Moreover,an annexed shear flow and a molecular-dispersion effect are found.The results demonstrate a useful strategy of this approach to study polymer flows and bring new insights into the non-Newtonian-fluid behaviors of bulk polymers in capillary rheometers and micro-fluidic devices.     

Melting behaviors of icosahedral metal clusters studied by Monte Carlo simulations

We present an atom‐resolved analysis method that traces physical quantities such as the root‐mean‐square bond length fluctuation and coordination number for individual atoms as functions of temperature or time. This method is applied to explain the temperature‐dependent behaviors of three types of Ni_N (N=12,13,14) clusters. The detailed studies for the three types of clusters reveal characteristics as follows: (a) as the temperature increases, all three types of clusters undergo two‐stage melting, irrespective of the existence of vacancy or adatom on the icosahedral surfaces, (b) the melting of icosahedral clusters with vacancy starts with vacancy hopping, which has not been observed for any type of small clusters (N<34), (c) the melting of the icosahedral clusters with adatom (N=14) is initiated by adatom hopping, followed by the site exchange between the adatom and surface atoms. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 380–387, 2000     

Titration of hydrophobic polyelectrolytes using Monte Carlo simulations

The conformation and titration curves of weak (or annealed) hydrophobic polyelectrolytes have been examined using Monte Carlo simulations with screened Coulomb potentials in the grand canonical ensemble. The influence of the ionic concentration pH and presence of hydrophobic interactions has been systematically investigated. A large number of conformations such as extended, pearl-necklace, cigar-shape, and collapsed structures resulting from the subtle balance of short-range hydrophobic attractive interactions and long-range electrostatic repulsive interactions between the monomers have been observed. Titration curves were calculated by adjusting the pH-pK(0) values (pK(0) represents the intrinsic dissociation constant of an isolated monomer) and then calculating the ionization degree alpha of the polyelectrolyte. Important transitions related to cascades of conformational changes were observed in the titration curves, mainly at low ionic concentration and with the presence of strong hydrophobic interactions. We demonstrated that the presence of hydrophobic interactions plays an important role in the acid-base properties of a polyelectrolyte in promoting the formation of compact conformations and hence decreasing the polyelectrolyte degree of ionization for a given pH-pK(0) value.     

Size and persistence length of molecular bottle-brushes by Monte Carlo simulations

Single-chain simulations of densely branched comb polymers, or "molecular bottle-brushes" with side-chains attached to every (or every second) backbone monomer, were carried out by off-lattice Monte Carlo technique. A coarse-grained model, described by hard spheres connected by harmonic springs, was employed. Backbone lengths of up to 100 units were considered, and compared with the corresponding linear chains. The backbone molecular size was investigated as a function of its length at fixed arm size, and as a function of the arm size at fixed backbone length. The apparent swelling exponents obtained by a power-law fit were found to be larger than those for the corresponding linear polymers, indicative of stiffening of the comb backbone. The probability distribution function for the backbone end-to-end distance was also investigated for different backbone lengths and arm sizes. Analysis of this function yielded the critical exponents, which revealed an increase in the swelling exponent consistent with values found from the molecular size. The apparent persistence length of the backbone was also determined, and was found to increase with increasing branching density. Finally, the static structure factors of the whole bottle-brushes and of their backbones are discussed, which provides another consistent estimate of the swelling exponents.     

Efficient Monte Carlo trial moves for polypeptide simulations

A new move set for the Monte Carlo simulations of polypeptide chains is introduced. It consists of a rigid rotation along the (C(alpha)) ends of an arbitrary long segment of the backbone in such a way that the atoms outside this segment remain fixed. This fixed end move, or FEM, alters only the backbone dihedral angles phi and psi and the C(alpha) bond angles of the segment ends. Rotations are restricted to those who keep the alpha bond angles within their maximum natural range of approximately +/-10 degrees. The equations for the angular intervals (tau) of the allowed rigid rotations and the equations required for satisfying the detailed balance condition are presented in detail. One appealing property of the FEM is that the required number of calculations is minimal, as it is evident from the simplicity of the equations. In addition, the moving backbone atoms undergo considerable but limited displacements of up to 3 A. These properties, combined with the small number of backbone angles changed, lead to high acceptance rates for the new conformations and make the algorithm very efficient for sampling the conformational space. The FEMs, combined with pivot moves, are used in a test to fold a group of coarse-grained proteins with lengths of up to 200 residues.     

Thermodynamic properties of van der Waals fluids from Monte Carlo simulations and perturbative Monte Carlo theory

Computer simulations have been performed for fluids with van der Waals potential, that is, hard spheres with attractive inverse power tails, to determine the equation of state and the excess energy. On the other hand, the first- and second-order perturbative contributions to the energy and the zero- and first-order perturbative contributions to the compressibility factor have been determined too from Monte Carlo simulations performed on the reference hard-sphere system. The aim was to test the reliability of this "exact" perturbation theory. It has been found that the results obtained from the Monte Carlo perturbation theory for these two thermodynamic properties agree well with the direct Monte Carlo simulations. Moreover, it has been found that results from the Barker-Henderson [J. Chem. Phys. 47, 2856 (1967)] perturbation theory are in good agreement with those from the exact perturbation theory.     

Confined crystallization of cylindrical diblock copolymers studied by dynamic Monte Carlo simulations

We report dynamic Monte Carlo simulations of polymer crystallization confined in the cylindrical microdomains of diblock copolymers. The microdomains were prepared via spontaneous microphase separation from homogeneous melt, and the major component was then frozen in a vitreous amorphous state to make a hard confinement to the crystallization of the minor component. We found that during the isothermal crystallization at high temperatures, crystal orientations are dominantly perpendicular to the cylinder axis at the early stage of crystal nucleation and remain to the final state; while if the block junctions are broken before crystallization, crystal orientations are dominantly parallel at the early stage of crystal nucleation, and eventually other orientations take the place of parallel preferences. Analysis of bond orientations in the heterogeneous melts demonstrates the microscopic origin of oriented crystal nucleation.