3 research outputs found
Maximum Margin Clustering for State Decomposition of Metastable Systems
When studying a metastable dynamical system, a prime concern is how to
decompose the phase space into a set of metastable states. Unfortunately, the
metastable state decomposition based on simulation or experimental data is
still a challenge. The most popular and simplest approach is geometric
clustering which is developed based on the classical clustering technique.
However, the prerequisites of this approach are: (1) data are obtained from
simulations or experiments which are in global equilibrium and (2) the
coordinate system is appropriately selected. Recently, the kinetic clustering
approach based on phase space discretization and transition probability
estimation has drawn much attention due to its applicability to more general
cases, but the choice of discretization policy is a difficult task. In this
paper, a new decomposition method designated as maximum margin metastable
clustering is proposed, which converts the problem of metastable state
decomposition to a semi-supervised learning problem so that the large margin
technique can be utilized to search for the optimal decomposition without phase
space discretization. Moreover, several simulation examples are given to
illustrate the effectiveness of the proposed method
Implications of PCCA+ in Molecular Simulation
Upon ligand binding or during chemical reactions the state of a molecular system changes in time. Usually we consider a finite set of (macro-) states of the system (e.g., ’bound’ vs. ’unbound’), although the process itself takes place in a continuous space. In this context, the formula χ=XA connects the micro-dynamics of the molecular system to its macro-dynamics. χ can be understood as a clustering of micro-states of a molecular system into a few macro-states. X is a basis of an invariant subspace of a transfer operator describing the micro-dynamics of the system. The formula claims that there is an unknown linear relation A between these two objects. With the aid of this formula we can understand rebinding effects, the electron flux in pericyclic reactions, and systematic changes of binding rates in kinetic ITC experiments. We can also analyze sequential spectroscopy experiments and rare event systems more easily. This article provides an explanation of the formula and an overview of some of its consequences