scholarly journals Bayesian inference of ocean diffusivity from Lagrangian trajectory data

2019 ◽  
Vol 140 ◽  
pp. 101401 ◽  
Author(s):  
Y.K. Ying ◽  
J.R. Maddison ◽  
J. Vanneste
2019 ◽  
Author(s):  
Hongbin Wan ◽  
Yunhui Ge ◽  
Asghar Razavi ◽  
Vincent A. Voelz

AbstractHydrogen/deuterium exchange (HDX) is a powerful technique to investigate protein conformational dynamics at amino acid resolution. Because HDX provides a measurement of solvent exposure of backbone hydrogens, ensemble-averaged over potentially slow kinetic processes, it has been challenging to use HDX protection factors to refine structural ensembles obtained from molecular dynamics simulations. This entails two dual challenges: (1) identifying structural observables that best correlate with backbone amide protection from exchange, and (2) restraining these observables in molecular simulations to model ensembles consistent with experimental measurements. Here, we make significant progress on both fronts. First, we describe an improved predictor of HDX protection factors from structural observables in simulated ensembles, parameterized from ultra-long molecular dynamics simulation trajectory data, with a Bayesian inference approach used to retain the full posterior distribution of model parameters.We next present a new method for obtaining simulated ensembles in agreement with experimental HDX protection factors, in which molecular simulations are performed at various temperatures and restraint biases, and used to construct multi-ensemble Markov State Models (MSMs). Finally, the BICePs algorithm (Bayesian Inference of Conformational Populations) is then used with our HDX protection factor predictor to infer which thermodynamic ensemble agrees best with experiment, and estimate populations of each conformational state in the MSM. To illustrate the approach, we use a combination of HDX protection factor restraints and chemical shift restraints to model the conformational ensemble of apomyoglobin at pH 6. The resulting ensemble agrees well with experiment, and gives insight into the all-atom structure of disordered helices F and H in the absence of heme.Graphical TOC Entry


2020 ◽  
Author(s):  
David Wichmann ◽  
Christian Kehl ◽  
Henk A. Dijkstra ◽  
Erik van Sebille

Abstract. The detection of finite-time coherent particle sets in Lagrangian trajectory data using data clustering techniques is an active research field at the moment. Yet, the clustering methods mostly employed so far have been based on graph partitioning, which assigns each trajectory to a cluster, i.e. there is no concept of noisy, incoherent trajectories. This is problematic for applications to the ocean, where many small coherent eddies are present in a large fluid domain. In addition, to our knowledge none of the existing methods to detect finite-time coherent sets has an intrinsic notion of coherence hierarchy, i.e. the detection of finite-time coherent sets at different spatial scales. Such coherence hierarchies are present in the ocean, where basin scale coherence coexists with smaller coherent structures such as jets and mesoscale eddies. Here, for the first time in this context, we use the density-based clustering algorithm OPTICS (Ankerst et al., 1999) to detect finite-time coherent particle sets in Lagrangian trajectory data. Different from partition based clustering methods, OPTICS does not require to fix the number of clusters beforehand. Derived clustering results contain a concept of noise, such that not every trajectory needs to be part of a cluster. OPTICS also has a major advantage compared to the previously used DBSCAN method, as it can detect clusters of varying density. Further, clusters can also be detected based on density changes instead of absolute density. Finally, OPTICS based clusters have an intrinsically hierarchical structure, which allows to detect coherent trajectory sets at different spatial scales at once. We apply OPTICS directly to Lagrangian trajectory data in the Bickley jet model flow and successfully detect the expected vortices and the jet. The resulting clustering separates the vortices and the jet from background noise, with an imprint of the hierarchical clustering structure of coherent, small scale vortices in a coherent, large-scale, background flow. We then apply our method to a set of virtual trajectories released in the eastern South Atlantic Ocean in an eddying ocean model and successfully detect Agulhas rings. At larger scale, our method also separates the eastward and westward moving parts of the subtropical gyre. We illustrate the difference between our approach and partition based k-Means clustering using a 2-dimensional embedding of the trajectories derived from classical multidimensional scaling. We also show how OPTICS can be applied to the spectral embedding of a trajectory based network to overcome the problems of k-Means spectral clustering in detecting Agulhas rings.


2021 ◽  
Vol 28 (1) ◽  
pp. 43-59
Author(s):  
David Wichmann ◽  
Christian Kehl ◽  
Henk A. Dijkstra ◽  
Erik van Sebille

Abstract. The detection of finite-time coherent particle sets in Lagrangian trajectory data, using data-clustering techniques, is an active research field at the moment. Yet, the clustering methods mostly employed so far have been based on graph partitioning, which assigns each trajectory to a cluster, i.e. there is no concept of noisy, incoherent trajectories. This is problematic for applications in the ocean, where many small, coherent eddies are present in a large, mostly noisy fluid flow. Here, for the first time in this context, we use the density-based clustering algorithm of OPTICS (ordering points to identify the clustering structure; Ankerst et al., 1999) to detect finite-time coherent particle sets in Lagrangian trajectory data. Different from partition-based clustering methods, derived clustering results contain a concept of noise, such that not every trajectory needs to be part of a cluster. OPTICS also has a major advantage compared to the previously used density-based spatial clustering of applications with noise (DBSCAN) method, as it can detect clusters of varying density. The resulting clusters have an intrinsically hierarchical structure, which allows one to detect coherent trajectory sets at different spatial scales at once. We apply OPTICS directly to Lagrangian trajectory data in the Bickley jet model flow and successfully detect the expected vortices and the jet. The resulting clustering separates the vortices and the jet from background noise, with an imprint of the hierarchical clustering structure of coherent, small-scale vortices in a coherent, large-scale background flow. We then apply our method to a set of virtual trajectories released in the eastern South Atlantic Ocean in an eddying ocean model and successfully detect Agulhas rings. We illustrate the difference between our approach and partition-based k-means clustering using a 2D embedding of the trajectories derived from classical multidimensional scaling. We also show how OPTICS can be applied to the spectral embedding of a trajectory-based network to overcome the problems of k-means spectral clustering in detecting Agulhas rings.


CICTP 2020 ◽  
2020 ◽  
Author(s):  
Zuyao Zhang ◽  
Li Tang ◽  
Yifeng Wang ◽  
Xuejun Zhang

Informatica ◽  
2019 ◽  
Vol 30 (1) ◽  
pp. 33-52 ◽  
Author(s):  
Pengfei HAO ◽  
Chunlong YAO ◽  
Qingbin MENG ◽  
Xiaoqiang YU ◽  
Xu LI

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