scholarly journals Ab Initio Models of Accreting Black Holes with Monte Carlo-based Relativistic Radiation Magnetohydrodynamics

2016 ◽  
Author(s):  
Joshua C. Dolence ◽  
Charles F. Gammie ◽  
Benjamin Ryan
Keyword(s):  
Black Holes ◽  
Monte Carlo ◽  
Ab Initio ◽  
Radiation Magnetohydrodynamics ◽  
Ab Initio Models

Quantifying electron-correlation effects in small coinage-metal clusters by ab initio calculations

2021 ◽  
Author(s):  
Victor Giovanni de Pina ◽  
Bráulio Gabriel Alencar Brito ◽  
Guo -Q Hai ◽  
Ladir Cândido
Keyword(s):  
Monte Carlo ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Electron Correlation ◽  
Metal Clusters ◽  
Correlation Effects ◽  
Diffusion Monte Carlo ◽  
Coinage Metal ◽  
Electron Correlation Effects ◽  
Fixed Node

We investigate many-electron correlation effects in neutral and charged coinage-metal clusters Cun, Agn, and Aun (n = 1 − 4) by ab initio calculations using fixed-node diffusion Monte Carlo (FN-DMC)...

scholarly journals A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

2021 ◽  
Vol 26 (2) ◽  
pp. 39
Author(s):  
Juan P. Sánchez-Hernández ◽  
Juan Frausto-Solís ◽  
Juan J. González-Barbosa ◽  
Diego A. Soto-Monterrubio ◽  
Fanny G. Maldonado-Nava ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Primary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Golden Ratio ◽  
Small Peptides ◽  
Hybrid Simulated Annealing ◽  
Ab Initio Models

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.

Constructing accurate interaction potentials to describe the microsolvation of protonated methane by helium atoms

2017 ◽  
Vol 19 (12) ◽  
pp. 8307-8321 ◽  
Author(s):  
Dennis Kuchenbecker ◽  
Felix Uhl ◽  
Harald Forbert ◽  
Georg Jansen ◽  
Dominik Marx
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Ab Initio ◽  
Path Integral ◽  
Interaction Potential ◽  
Stationary Point ◽  
Path Integral Monte Carlo ◽  
Interaction Potentials ◽  
Helium Atoms

An ab initio-derived interaction potential is derived and used in path integral Monte Carlo simulations to investigate stationary-point structures of CH5+ microsolvated by up to four helium atoms.

Structures and Photoelectron Spectroscopies of Si2C2-Studied with ab Initio Multicanonical Monte Carlo Simulation

1999 ◽  
Vol 103 (32) ◽  
pp. 6442-6447
Author(s):  
Pradipta Bandyopadhyay ◽  
Seiichiro Ten-no ◽  
Suehiro Iwata
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Ab Initio

Magnetic Phase Diagram of Transition Metal Doped ZnO from Density Functional Theory Calculations and Monte Carlo Simulations

2010 ◽  
Vol 1260 ◽  
Author(s):  
Sanjeev K. Nayak ◽  
Heike C. Herper ◽  
Peter Entel
Keyword(s):  
Monte Carlo ◽  
Curie Temperature ◽  
Monte Carlo Simulations ◽  
Ab Initio ◽  
Density Functional ◽  
Magnetic Phase Diagram ◽  
Density Functional Theory Calculations ◽  
Antiferromagnetic Coupling ◽  
Doped Zno ◽  
Co Concentrations

AbstractTransition metals doped ZnO are possible candidates for multiferroics. Here, we have investigated the evolution of ferromagnetism due to Co dopants. The magnetic properties have been studied for Co concentrations from 0 to 100% by using ab-initio methods, i.e., KKR Green's function techniques. In order to estimate the Curie temperature we have performed Monte Carlo simulations with ab-initio calculated exchange parameters.From our calculations the onset of ferromagnetism occurs between 5 to 20% of Co depending on the numerical details of KKR method used. For Co concentrations larger than 50% the system is dominated by antiferromagnetic coupling and no Curie temperature can be obtained.

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