scholarly journals Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding

2021 ◽  
Author(s):  
Zirui Zhang ◽  
Clarisse G. Ricci ◽  
Chao Fan ◽  
Li-Tien Cheng ◽  
Bo Li ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Level Set ◽  
Implicit Solvation ◽  
Biomolecular Binding

scholarly journals Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules

2009 ◽  
Vol 5 (2) ◽  
pp. 257-266 ◽  
Author(s):  
Li-Tien Cheng ◽  
Yang Xie ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon ◽  
Jianwei Che ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Level Set Method ◽  
Level Set ◽  
Implicit Solvation ◽  
Nonpolar Molecules

scholarly journals Application of the level-set method to the implicit solvation of nonpolar molecules

2007 ◽  
Vol 127 (8) ◽  
pp. 084503 ◽  
Author(s):  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon ◽  
Bo Li
Keyword(s):  
Level Set Method ◽  
Level Set ◽  
Implicit Solvation ◽  
Nonpolar Molecules

Simulation of Propagating Acoustic Wavefronts with Random Sound Speed

2014 ◽  
Vol 16 (4) ◽  
pp. 1081-1101
Author(s):  
Sheri L. Martinelli
Keyword(s):  
Monte Carlo ◽  
Level Set Method ◽  
Level Set ◽  
High Frequency ◽  
Sound Speed ◽  
Input Data ◽  
Eikonal Equation ◽  
Random Variables ◽  
Full Field ◽  
Sources Of Uncertainty

AbstractA method for simulating acoustic wavefronts propagating under random sound speed conditions is presented. The approach applies a level set method to solve the Eikonal equation of high frequency acoustics for surfaces of constant phase, instead of tracing rays. The Lagrangian nature often makes full-field ray solutions difficult to reconstruct. The level set method captures multiple-valued solutions on a fixed grid. It is straightforward to represent other sources of uncertainty in the input data using this model, which has an advantage over Monte Carlo approaches in that it yields an expression for the solution as a function of random variables.

scholarly journals Three-Dimensional Simulation of DRIE Process Based on the Narrow Band Level Set and Monte Carlo Method

Micromachines ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. 74 ◽  
Author(s):  
Jia-Cheng Yu ◽  
Zai-Fa Zhou ◽  
Jia-Le Su ◽  
Chang-Feng Xia ◽  
Xin-Wei Zhang ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Level Set ◽  
Narrow Band ◽  
Three Dimensional ◽  
Dimensional Simulation

Outbursts of comet Schwassmann-Wachmann 1, and the cloud of interplanetary boulders

1974 ◽  
Vol 22 ◽  
pp. 307 ◽  
Author(s):  
Zdenek Sekanina
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Interplanetary Space ◽  
Porous Matrix ◽  
Maximum Diameter ◽  
Expansion Velocity ◽  
Solid Constituent ◽  
Meteoric Material ◽  
Periodic Comet

AbstractIt is suggested that the outbursts of Periodic Comet Schwassmann-Wachmann 1 are triggered by impacts of interplanetary boulders on the surface of the comet’s nucleus. The existence of a cloud of such boulders in interplanetary space was predicted by Harwit (1967). We have used the hypothesis to calculate the characteristics of the outbursts – such as their mean rate, optically important dimensions of ejected debris, expansion velocity of the ejecta, maximum diameter of the expanding cloud before it fades out, and the magnitude of the accompanying orbital impulse – and found them reasonably consistent with observations, if the solid constituent of the comet is assumed in the form of a porous matrix of lowstrength meteoric material. A Monte Carlo method was applied to simulate the distributions of impacts, their directions and impact velocities.

Monte Carlo Algorithms for Moments of Transition Arrays

1988 ◽  
Vol 102 ◽  
pp. 79-81
Author(s):  
A. Goldberg ◽  
S.D. Bloom
Keyword(s):  
Monte Carlo ◽  
State Vector ◽  
Basis Vector ◽  
Collective State ◽  
Dispersion Characteristics ◽  
Dipole Strength ◽  
The Third ◽  
Monte Carlo Algorithms ◽  
Third Moment ◽  
Very High

AbstractClosed expressions for the first, second, and (in some cases) the third moment of atomic transition arrays now exist. Recently a method has been developed for getting to very high moments (up to the 12th and beyond) in cases where a “collective” state-vector (i.e. a state-vector containing the entire electric dipole strength) can be created from each eigenstate in the parent configuration. Both of these approaches give exact results. Herein we describe astatistical(or Monte Carlo) approach which requires onlyonerepresentative state-vector |RV> for the entire parent manifold to get estimates of transition moments of high order. The representation is achieved through the random amplitudes associated with each basis vector making up |RV>. This also gives rise to the dispersion characterizing the method, which has been applied to a system (in the M shell) with≈250,000 lines where we have calculated up to the 5th moment. It turns out that the dispersion in the moments decreases with the size of the manifold, making its application to very big systems statistically advantageous. A discussion of the method and these dispersion characteristics will be presented.

Electron Scattering in Solids

1990 ◽  
Vol 48 (2) ◽  
pp. 4-5
Author(s):  
Ryuichi Shimizu ◽  
Ze-Jun Ding
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Angular Distribution ◽  
Elastic Scattering ◽  
Electron Scattering ◽  
Cross Sections ◽  
Expansion Method ◽  
Electron Excitation ◽  
Partial Wave Expansion ◽  
Backscattered Electrons

Monte Carlo simulation has been becoming most powerful tool to describe the electron scattering in solids, leading to more comprehensive understanding of the complicated mechanism of generation of various types of signals for microbeam analysis.The present paper proposes a practical model for the Monte Carlo simulation of scattering processes of a penetrating electron and the generation of the slow secondaries in solids. The model is based on the combined use of Gryzinski’s inner-shell electron excitation function and the dielectric function for taking into account the valence electron contribution in inelastic scattering processes, while the cross-sections derived by partial wave expansion method are used for describing elastic scattering processes. An improvement of the use of this elastic scattering cross-section can be seen in the success to describe the anisotropy of angular distribution of elastically backscattered electrons from Au in low energy region, shown in Fig.l. Fig.l(a) shows the elastic cross-sections of 600 eV electron for single Au-atom, clearly indicating that the angular distribution is no more smooth as expected from Rutherford scattering formula, but has the socalled lobes appearing at the large scattering angle.

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