Background Markov state models have been widely used to study conformational changes of biologica... more Background Markov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dynamics. However, the solvent information in molecular simulations are often ignored in current methods, because of the large number of solvent molecules in a system and the indistinguishability of solvent molecules upon their exchange. Methods We present a solvent signature that compactly summarizes the ...
Suppose that ball-shaped sensors wander in a bounded domain. A sensor does not know its location ... more Suppose that ball-shaped sensors wander in a bounded domain. A sensor does not know its location but does know when it overlaps a nearby sensor. We say that an evasion path exists in this sensor network if a moving intruder can avoid detection. In ‘ Coordinate-free coverage in sensor networks with controlled boundaries via homology', Vin de Silva and Robert Ghrist give a necessary condition, depending only on the time-varying connectivity data of the sensors, for an evasion path to exist. Using zigzag persistent homology, we provide an equivalent condition that moreover can be computed in a streaming fashion. However, no method with time-varying connectivity data as input can give necessary and sufficient conditions for the existence of an evasion path. Indeed, we show that the existence of an evasion path depends not only on the fibrewise homotopy type of the region covered by sensors but also on its embedding in spacetime. For planar sensors that also measure weak rotation and...
The persistence barcode is a well-established complete discrete invariant for finitely generated ... more The persistence barcode is a well-established complete discrete invariant for finitely generated persistence modules [5] [1]. Its definition, however, does not extend to multi- dimensional persistence modules. In this paper, we introduce a new discrete invariant: the exterior critical series. This invariant is complete in the one-dimensional case and can be defined for multi-dimensional persistence modules, like the rank invariant [2]. However, the exterior critical series can detect some features that are not captured by the rank invariant.
Homology theory has been a very effective tool in the study of homotopy invariants for topologica... more Homology theory has been a very effective tool in the study of homotopy invariants for topological spaces. An important reason for this is the fact that it is often easy to compute homology groups. For instance, if one is given a finite simplicial complex, computing its ...
Background Markov state models have been widely used to study conformational changes of biologica... more Background Markov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dynamics. However, the solvent information in molecular simulations are often ignored in current methods, because of the large number of solvent molecules in a system and the indistinguishability of solvent molecules upon their exchange. Methods We present a solvent signature that compactly summarizes the ...
Suppose that ball-shaped sensors wander in a bounded domain. A sensor does not know its location ... more Suppose that ball-shaped sensors wander in a bounded domain. A sensor does not know its location but does know when it overlaps a nearby sensor. We say that an evasion path exists in this sensor network if a moving intruder can avoid detection. In ‘ Coordinate-free coverage in sensor networks with controlled boundaries via homology', Vin de Silva and Robert Ghrist give a necessary condition, depending only on the time-varying connectivity data of the sensors, for an evasion path to exist. Using zigzag persistent homology, we provide an equivalent condition that moreover can be computed in a streaming fashion. However, no method with time-varying connectivity data as input can give necessary and sufficient conditions for the existence of an evasion path. Indeed, we show that the existence of an evasion path depends not only on the fibrewise homotopy type of the region covered by sensors but also on its embedding in spacetime. For planar sensors that also measure weak rotation and...
The persistence barcode is a well-established complete discrete invariant for finitely generated ... more The persistence barcode is a well-established complete discrete invariant for finitely generated persistence modules [5] [1]. Its definition, however, does not extend to multi- dimensional persistence modules. In this paper, we introduce a new discrete invariant: the exterior critical series. This invariant is complete in the one-dimensional case and can be defined for multi-dimensional persistence modules, like the rank invariant [2]. However, the exterior critical series can detect some features that are not captured by the rank invariant.
Homology theory has been a very effective tool in the study of homotopy invariants for topologica... more Homology theory has been a very effective tool in the study of homotopy invariants for topological spaces. An important reason for this is the fact that it is often easy to compute homology groups. For instance, if one is given a finite simplicial complex, computing its ...
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