Hamiltonian replica exchange simulations of glucose oxidase adsorption on charged surfaces

2018 ◽  
Vol 20 (21) ◽  
pp. 14587-14596 ◽  
Author(s):  
Yun Xie ◽  
Zhanchao Li ◽  
Jian Zhou
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Glucose Oxidase ◽  
Replica Exchange ◽  
Hamiltonian Replica Exchange ◽  
Charged Surfaces ◽  
Replica Exchange Monte Carlo

Hamiltonian replica exchange Monte Carlo simulations efficiently identify the lowest-energy orientations of proteins on charged surfaces at variable ionic strengths.

scholarly journals Increasing the degree of parallelism using speculative execution in task-based runtime systems

2019 ◽  
Vol 5 ◽  
pp. e183 ◽  
Author(s):  
Bérenger Bramas
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
High Performance ◽  
Speculative Execution ◽  
Programming Models ◽  
Runtime Systems ◽  
Replica Exchange ◽  
Runtime System ◽  
Limited Degree ◽  
Replica Exchange Monte Carlo

Task-based programming models have demonstrated their efficiency in the development of scientific applications on modern high-performance platforms. They allow delegation of the management of parallelization to the runtime system (RS), which is in charge of the data coherency, the scheduling, and the assignment of the work to the computational units. However, some applications have a limited degree of parallelism such that no matter how efficient the RS implementation, they may not scale on modern multicore CPUs. In this paper, we propose using speculation to unleash the parallelism when it is uncertain if some tasks will modify data, and we formalize a new methodology to enable speculative execution in a graph of tasks. This description is partially implemented in our new C++ RS called SPETABARU, which is capable of executing tasks in advance if some others are not certain to modify the data. We study the behavior of our approach to compute Monte Carlo and replica exchange Monte Carlo simulations.

scholarly journals Monte Carlo estimation of the number of tatami tilings

2016 ◽  
Vol 27 (11) ◽  
pp. 1650128
Author(s):  
Kenji Kimura ◽  
Saburo Higuchi
Keyword(s):  
Monte Carlo ◽  
Replica Exchange ◽  
Exact Enumeration ◽  
Dual Lattice ◽  
Single Family ◽  
Dimer Model ◽  
Hamiltonian Replica Exchange ◽  
Replica Exchange Monte Carlo ◽  
Monte Carlo Estimation ◽  
Combinatorial Methods

Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local interaction on the dual lattice. We make use of a variant of the Hamiltonian replica exchange Monte Carlo method where data for ferromagnetic and anti-ferromagnetic models are combined to make a single family of histograms. The properties of the density of states is studied beyond exact enumeration and combinatorial methods. The logarithm of the number of the tilings is linear in the boundary length of the region for all the regions studied.

scholarly journals In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0133571 ◽  
Author(s):  
Anna Russo ◽  
Pasqualina Liana Scognamiglio ◽  
Rolando Pablo Hong Enriquez ◽  
Carlo Santambrogio ◽  
Rita Grandori ◽  
...  
Keyword(s):  
Monte Carlo ◽  
In Silico ◽  
Binding Protein ◽  
Maltose Binding Protein ◽  
Replica Exchange ◽  
Protein Ligands ◽  
Replica Exchange Monte Carlo
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