Multicanonical Monte Carlo calculation of the free‐energy map of the base–amino acid interaction

The specific interactions between base pairs and amino acids were studied by the multicanonical Monte Carlo method. We sampled numerous interaction configurations and side‐chain conformations of the amino acid by the multicanonical algorithm, and calculated the free energies of the interactions between an amino acid at given C_α positions and a fixed base pair. The contour maps of free energy derived from this calculation represent the preferred C_α position of the amino acid around the base, and these maps of various combinations of bases and amino acids can be used to quantify the specificity of intrinsic base–amino acid interactions. Similarly, enthalpy and entropy maps will provide further details of the specific interactions. We have also calculated the free‐energy map of the orientations of the C_α C_β bond vector, which indicates the preferential orientation of the amino acid against the base. We compared the results obtained by the multicanonical method with those of the exhaustive sampling and canonical Monte Carlo methods. The free‐energy map of the base–amino acid interaction obtained by the multicanonical simulation method was nearly identical to the accurate result derived from the exhaustive sampling method. This indicates that a single multicanonical Monte Carlo simulation can produce an accurate free‐energy map. Multicanonical Monte Carlo sampling produced free‐energy maps that were more accurate than those produced by canonical Monte Carlo sampling. Thus, the multicanonical Monte Carlo method can serve as a powerful tool for estimating the free‐energy landscape of base–amino acid interactions and for elucidating the mechanism by which amino acids of proteins recognize particular DNA base pairs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 954–962, 2000     

A Monte Carlo code to get response spectrum of ions for Neutron Depth Profiling

This paper presents a Monte Carlo code to get response spectrum of ions for the Neutron Depth Profiling (NDP) technique called Monte Carlo NDP (MC-NDP) that simulates the behavior of ions transmitted through a sample matrix and generates the energy spectrum for a specified detector. The MC-NDP model is based on the Ziegler–Biersack–Littmark Model, but incorporates the advantages of TRIM and CORTEO. The Impulse Approximation method is used to determine the flight length with the indexical interpolation method rather than the Magic algorithm for the scattering angle between ions and nucleus. This makes MC-NDP more efficient and convenient to simulate entire ion histories by a Monte Carlo approach. MC-NDP’s results agree well with both TRIM results and the experimental data.     

Monte Carlo simulation of bremsstrahlung emission by electrons

The basic components of Monte Carlo simulation of bremsstrahlung emission by electrons are presented. Various theoretical cross-sections that have been used in Monte Carlo codes are described and the emphasis is on the more accurate partial-wave cross-sections for which numerical databases are available. Sampling algorithms for a combination of numerical scaled energy-loss cross-sections and various analytical approximations to the intrinsic angular distribution are presented. Analogue simulation of the energy spectra and angular distribution of X rays from targets irradiated by electron beams is very inefficient and a simple variance-reduction technique, which is easy to implement and has proven to be particularly effective in speeding up these simulations, is described. Results from simulations of X-ray spectra with the general-purpose Monte Carlo code penelope are compared with experimental data for different materials and incident electrons with energies in the 20 keV to 1 GeV energy range.     

Electric-field-induced dissociation of heavy Rydberg ion-pair states

A classical trajectory Monte Carlo approach is used to simulate the dissociation of H(+)???F(-) and K(+)???Cl(-) heavy Rydberg ion pairs induced by a ramped electric field, a technique used experimentally to detect and probe ion-pair states. Simulations that include the effects of the strong short-range repulsive interaction associated with ion-pair scattering are in good agreement with experimental results for Stark wavepackets probed by a ramped field, demonstrating that many of the characteristics of field-induced dissociation can be well described using a quasi-classical model. The data also show that states with a given value of principal quantum number (i.e., binding energy) can dissociate over a broad range of applied fields, the exact field being governed by the initial orbital angular momentum and orientation of the state.     

Multiple scattering of light from polymer dispersed liquid crystal material

Light scattering from polymer dispersed liquid crystal (PDLC) material has been studied experimentally and by Monte Carlo simulation. Light scattering was measured as a function of both scattering angle and cell thickness. The cell thicknesses of practical interest are in an intermediate regime where neither single scattering nor light diffusion applies. Both the angular and the thickness dependence of the scattering intensity can be described accurately by a Monte Carlo simulation of multiple scattering from a homogeneous distribution of independent scatterers. The model smoothly interpolates between the single scattering limit for thin cells and the diffusion limit for thick cells. It can easily be extended to include any specific feature of a scattering display system.     

Monte‐Carlo simulation of x‐ray photoelectron emission from silver

Silver 3d x‐ray photoelectron spectroscopy (XPS) spectra were simulated with the Monte‐Carlo method using an effective energy‐loss function that was derived from a reflected electron energy‐loss spectroscopy (REELS) analysis based on an extended Landau approach. After confirming that Monte‐Carlo simulation based on the use of the effective energy‐loss function can successfully describe the experimental REELS spectrum and Ag 3d XPS spectrum, we applied Monte‐Carlo simulation to predict the angular distribution of Ag 3d x‐ray photoelectrons for different x‐ray incidence angles and different photoelectron take‐off angles. The experimental photoelectron emission microscope that we are constructing was confirmed as being close to the optimum configuration, in which the x‐ray incident angle as measured from the surface normal direction is 74° and the photoelectron take‐off angle is set normal to the surface. The depth distribution functions of the Ag 3d X‐ray photoelectrons for different energy windows suggest that the photoelectron emission microscope will exhibit greater surface sensitivity for narrower photoelectron energy windows. Copyright © 2003 John Wiley & Sons, Ltd.     

An improved dynamic Monte Carlo model coupled with Poisson equation to simulate the performance of organic photovoltaic devices

We describe a new dynamic Monte Carlo model to simulate the operation of a polymer-blend solar cell; this model provides major improvements with respect to the one we developed earlier [J. Phys. Chem. B 114, 36 (2010)] by incorporating the Poisson equation and a charge thermoactivation mechanism. The advantage of the present approach is its capacity to deal with a nonuniform electrostatic potential that dynamically depends on the charge distribution. In this way, the unbalance in electron and hole mobilities and the space-charge induced potential distribution can be treated explicitly. Simulations reproduce well the experimental I-V curve in the dark and the open-circuit voltage under illumination of a polymer-blend solar cell. The dependence of the photovoltaic performance on the difference in electron and hole mobilities is discussed.     

Free energies and phase equilibria of chain molecules

In this Article, a review is presented of recent developments in Monte Carlo simulations of chain molecules. The Rosenbluth chain insertion technique is used to calculate the free energy of the chain molecules. Furthermore, this insertion method is used to generate biased Monte Carlo moves. It is shown that this bias can be removed by adjusting the acceptance rules such that configurations are generated with their correct Boltzmann weight. This configurational-bias Monte Carlo method can be combined with the Gibbs-ensemble technique which results in an efficient method to simulate phase equilibria of chain molecules.     

Monte Carlo analyses of multiple backscattering of gamma rays

We have written a Monte Carlo code to simulate the experimental results of a previously reported study. We were able to analyse the energy distributions of photons that reached the detector system after suffering several successive Compton scatterings in the target. We have also investigated how the number of multiply backscattered events depends on the target thickness and the energy of the primary photons.     

X-ray treatment at 5 MeV and above

There is agreement in the scientific community that X-ray treatment of food at 7.5 MeV can be safe. Possible process improvements for treating at higher than 5 MeV X-rays have been re-visited. Monte Carlo methods have been applied to simulate the X-ray conversion process and to calculate dose distributions in homogeneous phantoms. Experimental data obtained using X-rays produced with a Rhodotron TT200 at 5 and 10 MeV verifies a representative set of data which is calculated with the presented method.

With this qualified Monte Carlo tool, calculations at 7.5 MeV incident electron energy were performed. The analysis gives special attention to higher photon yield, improved product penetration, as well as surface and edge effects.     

Photodissociation of alkyl iodides in helium nanodroplets. I. Kinetic energy transfer

The photodissociation of (fluorinated) alkyl iodides in helium nanodroplets at a wavelength of 266 nm has been investigated by means of ion imaging techniques. It is found that a significant fraction of the created fragments escapes from the helium droplets. The speed and kinetic energy distributions of these fragments are found to be notably modified with respect to the corresponding gas phase distributions. The fragments, furthermore, show a speed dependent angular distribution. The loss of kinetic energy as well as the reduction of the anisotropy parameter show a strong mass dependence. These observations point to a nonthermal escape process in which the kinetic energy and momentum transfer from the fragments to the solvent is governed by binary collisions with the individual helium atoms making up the droplet. Monte Carlo simulations based on hard-sphere binary collisions substantiate this interpretation of the data.     

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.     

Effective numbers of modes applied to analysis of internal dynamics of weakly bound clusters

The dependence of the volume of the chaotic component in the internal dynamics of triatomic van der Waals clusters on the angular momentum is calculated using the Monte Carlo and molecular dynamics methods. It has been found that this dependence is nonmonotonic and that its functional form varies for different values of the total energy. The effective number of rotational modes was used to clarify why a change in the volume of chaotic component of the phase space happens for certain values of the angular momentum. We conclude that a large fraction of regular trajectories in relation to all trajectories appears only when there is a possibility for the regular motion to perform a rotation different from that for a chaotic motion. When such difference is small, the regular motion disappears. The effective number of rotational modes can be used to estimate the difference in the type of rotation and is a convenient parameter which controls changes in the dynamics of the system.     

Photon-electron energy deposition in CANDU reactor channels: Simulation and modelling

Simulation of photon-electron transport in a CANDU reactor fuel channel using the Monte Carlo method for calculating the energy deposition in the coolant is studied. The geometry of the CANDU fuel channel is very complex so methods that make such simulations more practicable, without adversely affecting the results, are introduced. In this regard, the use of simplifying assumptions and simplified geometrical models on the performance of two different Monte Carlo codes has been compared. An ETRAN-based code (SANDYL), and the code EGS4 produced comparable results, although the former performs faster in accounting for low energy electrons. A simplified computational model is also introduced. This model is based on decoupling photon-electron transport simulations by the use of electron-energy-transfer functions. The results obtained using the model are successfully validated using the EGS4 and SANDYL codes. A significant computational speedup (about a factor of seven compared to Monte Carlo simulations) is achieved with this model.     

Monte Carlo transport of electrons and positrons through thin foils

In measurements on electrons traversing matter it is important to know the transmission through that medium, their path-lengths and their angular distribution through matter. This allows one to seek improvement in techniques which employ electrons, including medical applications and materials irradiation. This work presents a simulation of the transport of beams of electrons and positrons through thin foils using an analog Monte Carlo code that simulates in a detailed way every electron movement or interaction in matter. As those particles penetrate thin absorbers, it has been assumed that they interact with matter only through elastic scattering, with negligible energy loss. This type of interaction has been described quite precisely because its angular form influences very much the angular distribution of electrons and positrons in matter. With this code it has been calculated that the number of particles, with energies between 100 and 3000 keV, which are transmitted through different media of various thicknesses as well as their angular distributions, show good agreement with the experimental data. The discrepancies are less than 5% for thicknesses lower than about 30% of the corresponding range in the tested material. As elastic scattering is very anisotropic, its angular distribution resembles a collimated incident beam for very thin foils, becoming slowly more isotropic when absorber thickness is increased.     

Angular distribution of photoelectrons with regard to non-dipole effects in photoionization and elastic electron scattering in solids

The angular distribution of photoelectrons from a semi-infinite solid sample is considered with regard to non-dipole transitions in photoionization with polarized and unpolarized radiation and elastic scattering. Non-dipole transitions are taken into account up to the octupole approximation. Calculations were carried out based on transport theory and Monte Carlo methods. Good agreement between two independent approaches is obtained. All angular parameters, necessary to calculate the angular dependence of intensities of photoelectrons for all elements Z < 100 in a wide range of ionizing radiation energies, are calculated in the relativistic approximation.     

三原子反应散射内态角分布的准经典计算

本工作利用分子反应动力学的准经典理论计算了原子与双原子分子三维反应散射产物内态振转角分布, 并得出振动分支比这一重要动态学信息。计算采用了半经验的LEPS形式的解析势能面。初始碰撞参数利用普遍使用的Monte Carlo方法确定。本文给出F+H_2(D_2)→HF(DF)+H(D)反应的计算结果, 并与最新交叉分子束实验进行了广泛的比较, 得到完全一致的规律。     

Differential track structure of electrons in liquid water

The differential spectrum of energy loss events produced in liquid water by electrons has been calculated using a differential cross-section incorporating exchange and binding. The average energy loss in a single event is found to vary from about 28 to about 68 eV for 100 eV for 100 eV to 1 MeV electrons, respectively. All energy loss events above a certain level (set either to 1 or to 5 keV) are assumed to produce branch tracks, which are further degraded using a Monte Carlo technique. The total track averaged energy loss per event for a 1 MeV electron is found to be about 57 eV.     

Total and angular differential cross sections of electrons emitted in collision between antiprotons and helium atoms

We present total and angular differential single-ionization cross sections for antiproton–helium collisions in the energy range of 1–1000 keV within the framework of time-dependent coupled-channel-, a continuum distorted wave eikonal initial state and classical trajectory Monte Carlo methods. The results are compared with other theoretical results and experimental data.     

Markov chains of infinite order and asymptotic satisfaction of balance: application to the adaptive integration method

Adaptive Monte Carlo methods can be viewed as implementations of Markov chains with infinite memory. We derive a general condition for the convergence of a Monte Carlo method whose history dependence is contained within the simulated density distribution. In convergent cases, our result implies that the balance condition need only be satisfied asymptotically. As an example, we show that the adaptive integration method converges.