Building Markov state models using optimal transport theory

2019 ◽  
Vol 150 (5) ◽  
pp. 054105 ◽  
Author(s):  
Purushottam D. Dixit ◽  
Ken A. Dill
2018 ◽  
Author(s):  
Purushottam Dixit ◽  
Ken Dill

Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because<br>molecular simulations are slow to nd and sample the rare transient events. We describe here an e cient approximate way to determine MSM rate matrices by combining Maximum Caliber (maximizing path entropies) with Optimal Transport Theory (minimizing some path cost function, as when routing trucks on transportation<br>networks) to patch together transient dynamical information from multiple nonequilibrium<br>simulations. We give toy examples.


2018 ◽  
Author(s):  
Purushottam Dixit ◽  
Ken Dill

Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because<br>molecular simulations are slow to nd and sample the rare transient events. We describe here an e cient approximate way to determine MSM rate matrices by combining Maximum Caliber (maximizing path entropies) with Optimal Transport Theory (minimizing some path cost function, as when routing trucks on transportation<br>networks) to patch together transient dynamical information from multiple nonequilibrium<br>simulations. We give toy examples.


2021 ◽  
Vol 11 (9) ◽  
pp. 4070
Author(s):  
Rabiul Hasan Kabir ◽  
Kooktae Lee

This paper addresses a wildlife monitoring problem using a team of unmanned aerial vehicles (UAVs) with the optimal transport theory. The state-of-the-art technology using UAVs has been an increasingly popular tool to monitor wildlife compared to the traditional methods such as satellite imagery-based sensing or GPS trackers. However, there still exist unsolved problems as to how the UAVs need to cover a spacious domain to detect animals as many as possible. In this paper, we propose the optimal transport-based wildlife monitoring strategy for a multi-UAV system, to prioritize monitoring areas while incorporating complementary information such as GPS trackers and satellite-based sensing. Through the proposed scheme, the UAVs can explore the large-size domain effectively and collaboratively with a given priority. The time-varying nature of wildlife due to their movements is modeled as a stochastic process, which is included in the proposed work to reflect the spatio-temporal evolution of their position estimation. In this way, the proposed monitoring plan can lead to wildlife monitoring with a high detection rate. Various simulation results including statistical data are provided to validate the proposed work. In all different simulations, it is shown that the proposed scheme significantly outperforms other UAV-based wildlife monitoring strategies in terms of the target detection rate up to 3.6 times.


2021 ◽  
Author(s):  
Arghadwip Paul ◽  
Suman Samantray ◽  
Marco Anteghini ◽  
Mohammed Khaled ◽  
Birgit Strodel

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.


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