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At least 19 recordsLinked to original sources
PubMed1992

Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model.

The Monte Carlo dynamics method was used to examine the process of protein insertion into model cell membranes. The water and lipid environments were taken into account via an effective medium approximation based on coordinate-dependent hydrophobic and hydrogen bond potentials. The polypeptide chain was represented in a full-backbone atom representation as a chain of diamond lattice vectors. The simulations support the idea that to a good approximation insertion may be depicted as a spontaneous thermodynamic process. The mechanism of membrane insertion of a simple lattice protein chain exhibits many features of theoretical predictions and is in good accord with experimental data. In the model, insertion begins with adsorption of the chain onto the interface, followed by the formation of helical fragments. These fragments, having partially saturated internal hydrogen bonds, can be transported into the lipid phase and then form transbilayer structures.

Cell Membrane↗
PubMedDate not supplied

Monte Carlo calculation on trans/cis-polysarcosine.

Monte Carolo calculations were made on unperturbed trans-polysarcosine chain, non-self-intersecting trans-polysarcosine chain, and also non-self-intersecting trans/cis-polysarcosine chain by using a hard-sphere model. In the last case, an attempt was first made to introduce cis amide bond into the Monte Carlo calculation of polypeptide chain. Dipeptide energy maps for four different trans/cis dyad sequences were calculated. The allowed regions were consistent with the pairs of dihedral angles observed in cyclo-pentasarcosyl and cyclo-octasarcosyl. The mean-square end-to-end distance and higher even moments were obtained. The distribution function of the end-to-end distance was calculated from the even moments by using Nagai's equation and compared with the direct Monte Carlo data. The best agreement was obtained by cutting off the terms containing much higher order even moments than a critical order. The fractions of cis amide bond and of the four different trans/cis dyad sequences in polysarcosine were calculated. The results of calculation were compared with the 220-MHz NMR spectra of polysarcosine in three different solvents. Qualitative agreement was stained for longer chains.

Amides↗
PubMedDate not supplied

A standard timing benchmark for EGS4 Monte Carlo calculations.

A Fortran 77 Monte Carlo source code built from the EGS4 Monte Carlo code system has been used for timing benchmark purposes on 29 different computers. This code simulates the deposition of energy from an incident electron beam in a 3-D rectilinear geometry such as one would employ to model electron and photon transport through a series of CT slices. The benchmark forms a standalone system and does not require that the EGS4 system be installed. The Fortran source code may be ported to different architectures by modifying a few lines and only a moderate amount of CPU time is required ranging from about 5 h on PC/386/387 to a few seconds on a massively parallel supercomputer (a BBN TC2000 with 512 processors).

Electrons↗
PubMedDate not supplied

Monte Carlo advice.

The generation of long, high quality random number sequences for Monte Carlo simulations using minicomputers is considered. The importance of the thorough testing of Monte Carlo random number generators is emphasized. A recommendation is given to authors of Monte Carlo papers to specify their random number generator and to describe the randomness testing which that generator has undergone.

Computers↗
PubMed1992

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

A Monte Carlo quantum mechanical-molecular mechanical (QM-MM) simulation method was used to determine the contributions of the solvent polarization effect to the total interaction energies between solute and solvent for amino acid side chains and nucleotide bases in aqueous solution. In the present AM1-TIP3P approach, the solute molecule is characterized by valence electrons and nucleus cores with Hartree-Fock theory incorporating explicit solvent effects into the total Hamiltonian, while the solvent is approximated by the three-point charge TIP3P model. The polarization energy contributes 10 to 20 percent of the total electrostatic energy in these systems. The performance of the hybrid AM1-TIP3P model was further validated by consideration of bimolecular complexes with water and by computation of the free energies of solvation of organic molecules using statistical perturbation theory. Excellent agreement with ab initio 6-31G(d) results and experimental solvation free energies was obtained.

Acetates↗
PubMed1992

A Monte Carlo method for combined segregation and linkage analysis.

We introduce a Monte Carlo approach to combined segregation and linkage analysis of a quantitative trait observed in an extended pedigree. In conjunction with the Monte Carlo method of likelihood-ratio evaluation proposed by Thompson and Guo, the method provides for estimation and hypothesis testing. The greatest attraction of this approach is its ability to handle complex genetic models and large pedigrees. Two examples illustrate the practicality of the method. One is of simulated data on a large pedigree; the other is a reanalysis of published data previously analyzed by other methods.

Algorithms↗
PubMed1978

Interacting enzyme systems at steady state: further Monte Carlo calculations on two-state molecules.

In this work, Monte Carlo calculations were made on a 10 x 10 lattice of two-state, steady-state enzyme molecules in two special cases for which the Bragg-Williams (mean field) approximation had earlier produced some very interesting phase-transition properties. The Monte Carlo results proved to be similar to Bragg-Williams in some respects but not in others. The discrepancies are attributed primarily to; (i) inadequate treatment by Bragg-Williams of strong negative cooperativity; and (ii) the finite size of the 10 x 10 lattice used in the exact calculations.

Enzymes↗
PubMed1992

Spontaneous regression of residual tumour burden: prediction by Monte Carlo simulation.

Current cancer treatment protocols are designed to release the tumour burden down to a small number of cells. In this study, we use Monte Carlo simulations to show that small populations of cells with intrinsic cell loss rates comparable to the cell loss rates observed clinically in human tumours, may regress spontaneously. Large populations of cells tend to grow under the same conditions of cell loss that result in extinction of small clones. Furthermore, minor variations in the intrinsic cell death probability near 0.50 result in large differences in the number of surviving cells calculated at the 100th generation. When Monte Carlo simulations of clonal growth resulted in clones with large populations (> 50 cells), the population as a whole behaved in a deterministic fashion (logarithmic growth) similar to those observed in clinically observed neoplasms and consistent with other published models of tumour growth. These findings provide a plausible explanation for the clinically observed failure of tumours to recur in instances where tumour burden remains following cancer therapy. The findings also demonstrate the usefulness of the Monte Carlo method to simulate biologic events in populations where the fate of each member of a population can be modeled probabilistically.

Cell Death↗
PubMedDate not supplied

Intrachain reaction of a pair of reactive groups attached to polymer ends. II. Monte carlo study on the intrachain reaction proceeding on trans/cis-polysarcosine chain.

Monte Carlo calculation was performed to evaluate the ring-closure probability of short polysarcosine chains. Calculations were made for unperturbed trans- non-self-intersecting trans-, and non-self-intersecting trans- and non-self-intersecting trans/cis-polysarcosine chains. In the latter case, the main chain amide bond was allowed to take cis as well as trans conformations. The ring-closure probability for unperturbed trans-polysarcosine chains was found to be substantially greater than for non-self-intersecting trans chains. Virtually no difference was observed between the ring-closure probability was used to estimate the cyclization constant, i.e., the ratio of rate constant for the intramolecular reaction of the two groups attached to the polymer ends to that of the intermolecular one. The results were compared with the experimental data for the intrachain reaction proceeding on polysarcosine chain reported in the first paper of this series. The Monte Carlo results roughly reproduced the experimental data and the calculated chain length dependence was consistent with the observed one for longer chains.

Binding Sites↗
PubMed1992

Monte Carlo simulation of rodent carcinogenicity bioassays.

In this paper we describe a simulation, by Monte Carlo methods, of the results of rodent carcinogenicity bioassays. Our aim is to study how the observed correlation between carcinogenic potency (beta or 1n2/TD50) and maximum tolerated dose (MTD) arises, and whether the existence of this correlation leads to an artificial correlation between carcinogenic potencies in rats and mice. The validity of the bioassay results depends upon, among other things, certain biases in the experimental design of the bioassays. These include selection of chemicals for bioassay and details of the experimental protocol, including dose levels. We use as variables in our simulation the following factors: (1) dose group size, (2) number of dose groups, (3) tumor rate in the control (zero-dose) group, (4) distribution of the MTD values of the group of chemicals as specified by the mean and standard deviation, (5) the degree of correlation between beta and the MTD, as given by the standard deviation of the random error term in the linear regression of log beta on log (1/MTD), and (6) an upper limit on the number of animals with tumors. Monte Carlo simulation can show whether the information present in the existing rodent bioassay database is sufficient to reject the validity of the proposed interspecies correlations at a given level of stringency. We hope that such analysis will be useful for future bioassay design, and more importantly, for discussion of the whole NCI/NTP program.

Animals↗
PubMed1992

Monte Carlo studies of a model for lipid-gramicidin A bilayers.

This paper presents results of Monte Carlo simulations of a full bilayer of 200 lipid chains and one gramicidin A dimer. Simulations are described for systems with lipid chains of 14, 16, and 18 carbons, respectively. Using accepted potential functions to calculate interactions between all non-hydrogen atoms a Monte Carlo configuration sampling is generated from which order parameter profiles are calculated and specific configurations are displayed. Results are compared with experimental data for lipid-gramicidin bilayers.

Gramicidin↗
PubMed1977

A Monte Carlo computer model to investigate patient scheduling.

A Monte Carlo computer model was developed to investigate various types of patient appointment schedules for a single channel queue. Input parameters included the incidence of no-shows, the rate of unscheduled walk-ins, the frequency distribution of physician examination times, and the string of appointment times. The results included the frequency distributions of physician utilization rates and the total waiting time of all patients. Five hospital clinics were simulated. Even increment schedules yielded the best trade-off between physician utilization and patient waiting.

Appointments and Schedules↗
PubMed1977

Monte Carlo calculations of the energy response of lithium dosemeters to high energy electrons (less than 30 MeV).

Monte Carlo calculations of the energy response of LiF dosemeters have been carried out to help resolve the discrepancy between the measurements of Holt, Edelstein and Clark (1975) and those of Paliwal and Almond (1975) and others. It is concluded that the assumptions used by Holt et al. are largely responsible. They assume, in converting energy deposition in an air-filled ionization chamber to energy deposition in water, that as electrons penetrate a medium they are monoenergetic and the energy is given by Harder's expression (ICRU 1972). The assumption gives poor results as the stopping power for electrons in air is strongly energy dependent, and the energy spectrum has been significantly broadened. The Monte Carlo calculations are also used to criticize the electron cavity theories of Almond and McCray (1970), Burlin, Snelling and Owen (1969) and Holt et al. (1975), and to suggest as an alternative a slightly modified version of the Bragg-Gray theorem.

Electrons↗
PubMedDate not supplied

Monte Carlo calculations on polypeptide chains. VIII. Distribution functions for the end-to-end distance and radius of gyration for hard-sphere models of randomly coiling poly(glycine) and poly(L-alanine).

A Monte Carlo study of the distribution functions for the end-to-end distance and radius of gyration for hard-sphere models of poly(glycine) and poly(L-alanine) random coils has been conducted in the chain-length range n = 3 to 100 monomer units for both unperturbed chains and chains perturbed by long-range interactions (excluded volume effects). The distribution functions for the radius of gyration in all cases have been very precisely calculated, those for the perturbed end-to-end distance less precisely, and those for the unperturbed end-to-end distance least precisely. Empirical distribution functions of the form W(p) = ap-b exp(-cp-d) for the reduced end-to-end distance p = r/"r-2"-one-half and a similar form for the reduced radius of gyration could be least-squares fit to the Monte Carlo data. The expansion factors alpha-r and alpha-s were calculated vs. chain length and were used to test various versions of the two-parameter theory of the excluded volume effect. To be consistent with the chain-length dependence of alpha-r and alpha-s as determined by the Monte Carlo calculations, each of these theories required two different binary cluster integrals, a beta-r based on alpha-r and a beta-s based on alpha-s, both of which were strongly chain-length dependent. Both of these results suggest that the two-parameter theory is not applicable to the models used in this study. It was also found that, except for very short chain lengths, plots of ln alphs-r vs. ln n were linear, and thus that alpha-r could be estimated for long chain lengths. Comparison of these estimates with the experimental data on four polypeptide chains in one-earth solvents that the hard-sphere models used in this study yield expansion factors that do not seriously overestimate the magnitude of the excluded volume effect.

Alanine↗
PubMedDate not supplied

[Hydration of the left spiral of the poly-L-proline type. Study by the Monte Carlo method].

The paper exhibits results of hydration shell Monte Carlo calculations in poly-L-proline II and extended helix conformation and in alpha-helical and beta-structural conformations for comparison. It was found that left-handed helix of poly-L-proline II type as well as epsilon-helix are characterized by very favorable hydration. Therefore this conformation has preference as compared to other standard conformations of the main polypeptide chain. This determined inevitability of cold denaturation of protein.

Amino Acid Sequence↗
PubMed1992

Beta-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing.

A tertiary structure prediction is described using Monte Carlo simulated annealing for the peptide fragment corresponding to residues 16-36 of bovine pancreatic trypsin inhibitor (BPTI). The simulation starts with randomly chosen initial conformations and is performed without imposing experimental constraints using energy functions given for generic interatomic interactions. Out of 20 simulation trials, seven conformations show a sheet-like structure--two strands connected by a turn--although this sheet-like structure is not as rigid as that observed in native BPTI. It is also shown that these conformations are mostly looped and exhibit a native-like right-handed twist. Unlike the case with the C-peptide of RNase A, no conspicuous alpha-helical structure is found in any of the final conformations obtained in the simulation. However, the lowest-energy conformation does not resemble exactly the native structure. This indicates that the rigid beta-sheet conformation of native BPTI merely corresponds to a local minimum of the energy function if the fragment with residues 16-36 is isolated from the native protein. A statistical analysis of all 20 final conformations suggests that the tendency for the peptide segments to form extended beta-strands is strong for those with residues 18-24, and moderate for those with residues 30-35. The segment of residues 25-29 does not tend to form any definite structure. In native BPTI, the former segments are involved in the beta-sheet and the latter in the turn. A folding scenario is also speculated from this analysis.

Algorithms↗
PubMedDate not supplied

Calibration of parallel-plate chambers: resolution of several problems by using Monte Carlo calculations.

For five commonly used parallel-plate ion chambers, Monte Carlo calculations are presented of the wall attenuation and scatter correction factors (Kwall = Awall-1 or katt-1) and the correction for nonhomogeneous composition of the chamber (Kcomp or related to km). The chambers are assumed to have 0.5 g/cm2 buildup caps made of the predominant material in each chamber. These correction factors are needed if air-kerma calibration factors are used to deduce the chamber's cavity-gas calibration factor, Ngas. The scatter from the material around the cavity more than compensates for the attenuation in the front wall and hence Kwall values are less than unity. The corrections for the nonhomogeneous composition can be significant. Thin collectors or insulators behind the collecting volume can have a major effect because electron backscattering depends strongly on material. The calculations agree well with experimental data and explain previous results that had not been understood. Calculations for different buildup caps predict trends in chamber in-air responses, which go in the opposite direction to the km values for homogeneous chambers of the same materials. It is argued that Pwall, the wall correction factor for photon-beam measurements in-phantom is, to first order, the same correction factor as Kcomp, calculated for a buildup cap of the same material as the phantom material and the initial assumption that the wall material is made of the same material. Hence, Pwall can also be significantly different from unity. Recommended values of kmkatt or the equivalent Ngas/Nx, and Pwall (in 60Co beams) are presented for the 5 chambers. These values treat the Exradin P11, Markus and Holt parallel-plate chambers as homogeneous in construction whereas the values for the NACP and Capintec PS-033 chambers demonstrate that the chambers are distinctly nonhomogeneous.

Calibration↗
PubMedDate not supplied

Monte Carlo calculations on polypeptide chains. IX. A study of the effect of long-range interactions on the helix-coil transition.

A Monte Carlo statistical mechanical study of the helix-coil transition for a hard-sphere model of poly(L-alanine) has been conducted base on the theory of Lifson and Roig but including the effects of long-range interactions. A stochastic model of the kinetics of the helix-coil transition is presented, and a Monte Carlo stimulation of the kinetics based on this model was used to generate equilibrium chain samples, each chain of which consisted of Lifson-Roig weighted sequences of helix and coil residues. Each of the chains in this sample was then used many times by assigning at random specific sterically allowed coil states from a hard-sphere Ramachandran dipeptide map. Unperturbed properties were then calculated using this sample and perturbed properties by using only the non-self-conflicting subset. The properties calculated were the average degree of hydrogen bonding, the average length of a helical sequence, the mean-square end-to-end distance, the mean-square radius of gyration, and the distribution functions for the end-to-end distance and radius of gyration. This study was conducted at chain lengths 10, 34, and 85 residues. Helix-coil transition theory was fit to the perturbed transition curves in an attempt to ascertain if theory could then predict the perturbed values of the dimensions. For the hard-sphere model used in these calculations, it was found that current helix-coil transition theory does not predict the correct perturbed dimensions.

Kinetics↗