Monte Carlo Statistical Method Research Articles

The solvent effect in enzyme-substrate interactions: Models of carboxypeptidase

The structure of water in the active site of carboxypeptidase A is being studied with ab initio quantum mechanical calculations and with the Monte Carlo statistical method. The zinc-containing portion of the active site was modeled by [Zn(NH3)2(OH)]+ in a geometry taken from the crystal structure of the enzyme. The potential energy surface was probed by calculating the interaction energy of the model with a water molecule situated at 211 representative positions. Energy points were fit to an analytical expression that was used to determine cross-sectional contour maps of one water molecule moving on the fitted potential energy surface. Expansion of the active site model to include other catalytically important functional groups showed the specific contribution of each to the interaction potential. The analytical potentials were also used in a Monte Carlo simulation of the solvent structure in the active site of carboxypeptidase A. Preliminary results from the last iteration of a Monte Carlo calculation on a portion of the active site indicate a distribution of water molecules that is consistent with experimental data on the native enzyme, and with the inferences drawn from these model studies with single water molecules.

Numerical simulation of shock wave propagation in microchannels using continuum and kinetic approaches

Numerical simulations of shock wave propagation in microchannels and microtubes (viscous shock tube problem) have been performed using three different approaches: the Navier–Stokes equations with the velocity slip and temperature jump boundary conditions, the statistical Direct Simulation Monte Carlo method for the Boltzmann equation, and the model kinetic Bhatnagar–Gross–Krook equation with the Shakhov equilibrium distribution function. Effects of flow rarefaction and dissipation are investigated and the results obtained with different approaches are compared. A parametric study of the problem for different Knudsen numbers and initial shock strengths is carried out using the Navier–Stokes computations.

Uncertainty Evaluation of Human Risk Analysis (HRA) of Chemicals by Multiple Exposure Routes

The application of an ISO standard procedure (Guide to the Expression of Uncertainty in Measurement (GUM)) is here discussed to quantify uncertainty in human risk estimation under chronic exposure to hazardous chemical compounds. The procedure was previously applied to a simple model; in this article a much more complex model is used, i.e., multiple compound and multiple exposure pathways. Risk was evaluated using the usual methodologies: the deterministic reasonable maximum exposure (RME) and the statistical Monte Carlo method. In both cases, the procedures to evaluate uncertainty on risk values are detailed. Uncertainties were evaluated by different methodologies to account for the peculiarity of information about the single variable. The GUM procedure enables the ranking of variables by their contribution to uncertainty; it provides a criterion for choosing variables for deeper analysis. The obtained results show that the application of GUM procedure is easy and straightforward to quantify uncertainty and variability of risk estimation. Health risk estimation is based on literature data on a water table contaminated by three volatile organic compounds. Daily intake was considered by either ingestion of water or inhalation during showering. The results indicate one of the substances as the main contaminant, and give a criterion to identify the key component on which the treatment selection may be performed and the treatment process may be designed in order to reduce risk.

Effect of the accommodation coefficient on transfer processes in a supersonic rarefied gas flow around a transversely aligned cylinder

A supersonic flow around a cylinder is studied by the direct statistical Monte Carlo method in a wide range of rarefaction: from regimes close to continuum to free-molecular flow. The effect of the accommodation coefficient on the flow near the cylinder and on heat transfer between the gas and the cylinder is examined.

Parametric study of radiative heat transfer in participating gas–solid flows

Generally, before building a radiative model for a particular gas–solid flow, one has to determine whether the influence of particle scattering and gas radiation are significant. This paper gives the results of parametric studies on the influence of scattering and gas radiation for various gas–solid slabs at high temperature. A statistical Monte-Carlo method has been used in order to solve the radiative transfers into an emitting, absorbing and anisotropically scattering one-dimensional medium. These slabs are constituted of H 2O and CO 2 gases with a monodispersion of spherical particles. In a first step, Planck means of particle radiative properties of absorption and scattering have been studied at high temperature versus the diameter ( 10 −7 < D < 2.10 −4 m ) and the complex refractive index ( n = 1.7 or 2.5 and 10 −4 < k < 20 ). Then, fluxes emitted by numerous slabs have been computed and compared to emphasize the role of gases and particles. These fluxes are emitted by slabs with different thicknesses ( e = 0.1 m or 1 m), volume fraction ( 10 −7 < f v < 10 −3 ) and refractive index. In addition, particular attention is devoted to the use of the presented sensitivity results. An approach is then derived which permits to extend these results to other situations than those considered in this paper. Finally, the influence of the gas mixture and scattering on spectral emission is studied spectrally.

AgNOR cut‐point to distinguish mild and moderate epithelial dysplasia

Distinguishing mild and moderate epithelial dysplasia is difficult and controversial. We demonstrated earlier that silver-stainable nucleolar organizer region (AgNOR) is a simple, inexpensive and quantifiable method which can standardize this distinction reliably. To establish a cut-point mean AgNOR count for epithelial dysplasia validated by bootstrapping. One hundred oral leukoplakia biopsies at Dr R. Ahmed Dental College, Kolkata, India, examined for epithelial dysplasia using standard method (gold standard) were assessed for their mean AgNOR counts. A cut-point was selected employing receiver operating characteristic (ROC) curve. This estimate was stabilized by 10 000 resamples (with replacement) using parametric and non-parametric bootstrap, a Monte Carlo statistical method, corrected for bias to estimate standard errors (SE) of cut-point. Area under the curve (AUC) was 74%; non-parametric method suggested mean AgNOR cut-point = 2.42 AgNORs/nucleus; parametric method suggested cut-point = 2.57. The cut-point 95% confidence intervals (CIs) (bias corrected and accelerated) from parametric method (2.31; 2.66) was lower than non-parametric (2.43; 2.82). Applying a conservative paradigm, taking the lowest of all bootstrap 95% CIs, we suggest that mean AgNOR count of 2.3 be used as a cut-point for distinguishing between mild and moderate dysplasia. This strategy will provide an inexpensive, meaningful, definitive, reproducible and consistent diagnostic test for epithelial dysplasia.

Quantitative estimation of uncertainty in human risk analysis

This paper is aimed to candidate the use of an ISO standard procedure (Guide to the Expression of Uncertainty in Measurement, GUM) for quantitative evaluation of uncertainty in Human Risk estimation under chronic exposure to a hazardous chemical compound. Risk was evaluated by using the usual methodologies: the deterministic reasonable maximum exposure (RME) and the statistical Monte Carlo method; in both cases the procedures to evaluate the uncertainty on risk values are detailed. The paper put in evidence that the procedure is able to single out the variables that contribute mostly to the uncertainty. The obtained results show that the application of GUM procedure is easy and straightforward to estimate the uncertainty value on the results of risk estimation. The procedure is applied to a real case concerning the ingestion of milk contaminated by dioxins in a northern part of Italy; the risk value resulted to be over the minimal threshold of 10 −6 with 20–80% confidence.

Estimation of diffusion parameters in functionalized silicas with modulated porosity: Part II: Pore network modeling

In this work, the pore structure of those five (5) silicas SiO 2–X (see Part I) which have suffered gradual functionalization with functional groups X of increasing length (X = Ø, ≡Si–H, ≡Si–CH 2OH, ≡Si–(CH 2) 3OH, ≡Si–(CH 2) 11CH 3), is modeled as a three-dimensional cubic network of cylindrical pores. Those hybrids organic–inorganic SiO 2–X samples are characterized by different extent of pore blocking effects. The pores of samples are represented in a 9 × 9 × 9 lattice by the nodes as well the bonds that are interconnected in a so-called dual site-bond model, DSBM, network. The pore network is developed using a Monte Carlo statistical method where the cylindrical pores (nodes and bonds) are randomly assigned into the lattice, until matching of the theoretical results to the experimental data of N 2 adsorption–desorption measurements. Thus, a visual picture of the porous solid is possible. This realistic network is used next in order to study the steady-state gas transport (Knudsen gas-phase and viscous diffusion) properties for the examined materials and how flow processes depend on the morphology of the pore structure. The pore diffusivity D p and total permeability P of each porous medium is determined based on theoretical calculations and the structural statistical parameters, such as porosity ɛ p, tortuosity factor τ and connectivity c of pores is discussed with the corresponding experimental data described in Part I of this work. The results indicate clearly that the diffusion model made it possible to predict pore effective diffusivity in these porous media in very good agreement with the corresponding experimental results for all the examined solids (Part I). The pore diffusivity increases significantly as the value of the pore connectivity increases but the transport properties of the network are influenced strongly at lowest connectivity. Also the predicted tortuosity factor is related inversely to the extent of interconnection of pores in these solids, which indicates that the influence of pore branching to the tortuosity factor of the pore network decreases, as connectivity increases.

Statistical analysis of antenna robustness

This work presents a methodology for the evaluation of antenna susceptibility to various types of random physical damage. A Monte Carlo statistical method is proposed to estimate antenna parameters for different damage levels. A virtual experiment is used in order to avoid lengthy experimental trials. Antenna parameters are modeled for each randomly generated damage pattern. Statistical post processing with the Bootstrap method evaluates the parameters acquired from the antenna modeling software. To illustrate the methodology a comparative study of the Input Return Loss for the damage inflicted upon a planar dipole and a bow-tie antenna is made. The median value is estimated to describe the typical behavior of the antenna. With taken assumptions, Input Return Loss for the Bow-tie antenna is found more sensitive to partial damage.

Statistical modeling of thermal radiation transfer in buoyant turbulent diffusion flames

A statistical (Monte Carlo) method for radiative heat transfer has been incorporated in CFD modeling of buoyant turbulent diffusion flames in stagnant air and in a cross-wind. The model and the computational tool have been developed and applied to simulate both burner flames with controlled fuel supply rate and in self-sustained pool fires with burning rates coupled with flame radiation. The gas–soot mixture was treated either as gray (using the effective absorption coefficient derived from total emissivity data or the Planck mean absorption coefficient) or as non-gray (using the weighed sum of gray gases model). The comparison of predicted radiative heat fluxes indicates applicability of the gray media assumption in modeling of thermal radiation in case of high soot content. The effect of turbulence-radiation interaction is approximately taken into account in calculation of radiation emission, which is corrected to allow for temperature self-correlation and absorption-temperature correlation. In modeling buoyant propane flames in still air above 0.3 m diameter burner, extensive comparison is presented of the predictions with the measurements of gas species concentrations, temperature, velocity and their turbulent fluctuations, and radiative heat fluxes obtained in flames with different heat release rates. Similar to previously published experimental data, the predicted burning rate of flames above the acetone pools exposed to flame radiation increases with the pool diameter and approaches a constant level for large pool sizes. The magnitude of predicted burning rates is shown to be in agreement with the reported measurements. Augmentation of burning rate of the pool fire in a cross-wind because of increased net radiative heat flux received by the fuel surface and non-monotonic dependence of burning rate on cross-wind velocity, subject to the pool diameter, is predicted. The statistical treatment of thermal radiation transfer has been found to be robust and computationally efficient.

Surface magnetism of vanadium-based binary alloys: first principles investigations

Surface magnetism of vanadium-based disordered binary alloys V-Me (Me=Pd, Mo) has been studied by means of the first-principles LMTO-GF-CPA and fixed spin moment methods in conjunction with statistical Monte-Carlo method. Both systems are nonmagnetic in the bulk. However, we have shown that the (1 0 0) surface of uniformly random alloys is magnetic, and magnetic moment may also be present in segregated V-Mo alloys. The origin of the onset of surface magnetism in the studied alloys is analyzed.

STATISTICAL ENERGY ANALYSIS OF COUPLED PLATE SYSTEMS WITH LOW MODAL DENSITY AND LOW MODAL OVERLAP

Finite element methods, experimental statistical energy analysis (ESEA) and Monte Carlo methods have been used to determine coupling loss factors for use in statistical energy analysis (SEA). The aim was to use the concept of an ESEA ensemble to facilitate the use of SEA with plate subsystems that have low modal density and low modal overlap. An advantage of the ESEA ensemble approach was that when the matrix inversion failed for a single deterministic analysis, the majority of ensemble members did not encounter problems. Failure of the matrix inversion for a single deterministic analysis may incorrectly lead to the conclusion that SEA is not appropriate. However, when the majority of the ESEA ensemble members have positive coupling loss factors, this provides sufficient motivation to attempt an SEA model. The ensembles were created using the normal distribution to introduce variation into the plate dimensions. For plate systems with low modal density and low modal overlap, it was found that the resulting probability distribution function for the linear coupling loss factor could be considered as lognormal. This allowed statistical confidence limits to be determined for the coupling loss factor. The SEA permutation method was then used to calculate the expected range of the response using these confidence limits in the SEA matrix solution. For plate systems with low modal density and low modal overlap, relatively small variation/uncertainty in the physical properties caused large differences in the coupling parameters. For this reason, a single deterministic analysis is of minimal use. Therefore, the ability to determine both the ensemble average and the expected range with SEA is crucial in allowing a robust assessment of vibration transmission between plate systems with low modal density and low modal overlap.

DSMC simulation of the vertical structure of planetary rings

A statistical Monte Carlo method (DSMC) is developed to simulate granular flows occurring in dense planetary rings. The accuracy of the method is assessed through a comparison with existing molecular dynamics simulations of the vertical structure of planetary rings with and without self-gravity eects.

Startup analysis of oil-fired furnace – the smoothing Monte Carlo model approach

A multi-dimensional mathematical thermal model of the oil-fired furnace has been developed. Radiation calculation of this model is based on the Hottel's zone method incorporating with the statistical Monte Carlo method to determine the total exchange areas. The whole furnace is divided into 4 gaseous zones and 18 surface zones. The Monte Carlo method integrated with the least square smoothing technique considering both conservation and reciprocity is used to evaluate the total exchange areas, i.e. surface–surface, surface–gas, gas–gas and gas–surface, directly for both the absorbing and emitting media. A better accuracy is achieved in the determination of the total exchange areas by using the proposed smoothing Monte Carlo method.

Estimation of binding affinities for HEPT and nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations.

The interactions and energetics associated with the binding of 20 HEPT and 20 nevirapine nonnucleoside inhibitors of HIV-1 reverse transcriptase (RT) have been explored in an effort to establish simulation protocols and methods that can be used in the development of more effective anti-HIV drugs. Using crystallographic structures as starting points, all 40 inhibitors were modeled in the bound and unbound states via Monte Carlo (MC) statistical mechanics methods. Potentially useful descriptors of binding affinity were configurationally averaged for each inhibitor during the MC simulations, and correlations were sought with reported experimental activities. A viable regression equation was obtained using only four descriptors to correlate the 40 experimental activities with an r(2)() of 0.75 and cross-validated q(2)() of 0.69. The computed activities show a rmsd of 0.94 kcal/mol in comparison with experiment and an average unsigned error of 0.69 kcal/mol. The MC results reveal three physically reasonable parameters that control the binding affinities: (1) loss of hydrogen bonds with the inhibitor is unfavorable, (2) burial of hydrophobic surface area is favorable, and (3) a good geometrical fit without steric clashes is needed for the protein-inhibitor complex. It is gratifying that the corresponding descriptors are statistically the most important quantities for determining the anti-HIVRT activity for the 40 compounds. Representative examples are also given in which structural and thermodynamic information from the MC simulations is used to help understand binding differences for related compounds. A key pi-type hydrogen bond has been identified between secondary-amide nevirapine analogues and Tyr188A of HIVRT that explains their otherwise surprising activity and the ineffectiveness of nevirapine against the Y188C mutant.

Microclustering of TEL-AML1 translocation breakpoints in childhood acute lymphoblastic leukemia.

TEL-AML1 fusions are the most common chromosome translocations in childhood leukemia and often, if not always, occur in utero. We previously reported the genomic sequencing of nine TEL-AML1 translocations and showed unique structural features of a breakpoint cluster region in TEL intron 5. We now report data on sequencing and mapping of TEL-AML1 from an additional 11 patients and, using Monte Carlo statistical methods, have analyzed the intronic distribution of the 24 TEL-AML1 fusion junctions sequenced to date. Compared to a null hypothesis of random breakpoint allocation within TEL intron 5 and AML1 introns 1 and 2, significant microclustering was evident on both TEL and AML1. In contrast to previous reports, the two strongest microclusters on TEL were 3' to an unstable repeat region. AML1 demonstrated four highly significant microclusters, two of which were proximal to exons. We note the necessity of sequencing multiple breakpoints before the description of putative microcluster regions. TEL-AML1 breakpoints may be distributed into microclusters because of specific DNA sequence or chromatin features in susceptible cells. We also report on additional features of breakpoints, including a complex t(12;3;21) in one patient and an inverted sequence in another.

Familial influences on cortical evoked potentials in migraine.

Cortical information processing in migraine patients is impaired between attacks, showing deficient habituation of pattern-reversal visual evoked potentials (VEP), and strong intensity dependence of auditory cortical evoked potentials (IDAP). This could be a genetic trait as certain genetic patterns are known for evoked potentials in healthy subjects. We investigated VEP habituation and IDAP in 20 pairs of migraineurs made up of parents and their children. Using a Monte-Carlo statistical method, we selectively assessed vertical familial influences. VEP habituation and IDAP were abnormal in both parents and children. However, similarity was far more pronounced between related pairs than between unrelated pairs. Familial influences are highly significant in determinants of cortical information processing in migraineurs, hence supporting the important role of genetic factors.

Use of line surge arresters for the improvement of the lightning performance of 63 kV and 90 kV shielded and unshielded transmission lines

The lightning performance of 63 kV and 90 kV shielded and unshielded power transmission lines, protected by surge arresters are considered. A specialized software package is used for the computation of the line's fast front transients. A Monte Carlo statistical method, together with a three-dimensional electrogeometric model is used to determine the lightning stroke locations. Different arrester installation configurations are analyzed and compared. The energy duties of the transmission line surge arresters are computed statistically.

Continuum and kinetic approaches to the simulation of the hypersonic flow past a flat plate

The data of a mathematical simulation of hypersonic flow past a flat plate at zero incidence obtained on the basis of a numerical solution of the complete Navier-Stokes equations and the Monte Carlo statistical modeling method are compared. The effect of the slip and temperature jump conditions imposed on the body surface is examined for various values of the temperature factor. The behavior of the gasdynamic variables on the body surface and in the flowfield is analyzed.

高燃焼度（長寿命）高速炉混合酸化物燃料の設計成立性評価

The potential of the Mixed Oxide (MOX) fuel to achieve a high burnup and long life core was studied for four type fuels with the fuel performance code LIFE-IV. Operating conditions, uncertainties and tolerances were varied in calculations and the results were used to establish multi-dimensional response surfaces from the important performance parameters. The Monte Carlo statistical simulation method was applied to determine the effect of statistical tolerance and uncertainty distributions on the fuel performance and to obtain statistical chracteristic of the fuel behavior.(1) From low to medium burnups of 0-100 GWd/t, fission gas swelling dominates Fuel Cladding Mechanical Interaction (FCMI).(2) At high burnup of 150 to 200GWd/t, solid fission product swelling dominates FCMI and fuel performance characteristics are simplified because cladding strain proceeds approximately at a constant rate with burnup.(3) Statistical fuel performance characteristics were evaluated and it was ascertained that MOX has a potential to realize high burnup with 2-σ reliability.(4) The operatioal and fabricational tolerances have little effects on fuel performances.