This paper presents a 2×2 dynamical system to study the cyclic appearance and disappearance of the gas phase in a two-component (CO2, H2O), two phase (gas, liquid) flow in a single pore. Depending on injection rate, linearization of the dynamical system around equilibrium shows that the gas phase can exhibit two behaviors, either cyclically vanishing and appearing, or approaching a steady-state volume value. Numerical simulations were also run on the fully non-linear dynamical system to verify the results of the linearized model.

We study generalized Hopf–Cole transformations motivated by the Schrödinger bridge problem, which can be seen as a boundary value Hamiltonian system on the Wasserstein space. We prove that generalized Hopf–Cole transformations are symplectic submersions in the Wasserstein symplectic geometry. Many examples, including a Hopf–Cole transformation for the shallow water equations, are given. Based on this transformation, energy splitting inequalities are provided.

Multistep cell fate transitions with stepwise changes of transcriptional profiles are common to many developmental, regenerative and pathological processes. The multiple intermediate cell lineage states can serve as differentiation checkpoints or branching points for channeling cells to more than one lineages. However, mechanisms underlying these transitions remain elusive. Here, we explored gene regulatory circuits that can generate multiple intermediate cellular states with stepwise modulations of transcription factors. With unbiased searching in the network topology space, we found a motif family containing a large set of networks can give rise to four attractors with the stepwise regulations of transcription factors, which limit the reversibility of three consecutive steps of the lineage transition. We found that there is an enrichment of these motifs in a transcriptional network controlling the early T cell development, and a mathematical model based on this network recapitulates multistep transitions in the early T cell lineage commitment. By calculating the energy landscape and minimum action paths for the T cell model, we quantified the stochastic dynamics of the critical factors in response to the differentiation signal with fluctuations. These results are in good agreement with experimental observations and they suggest the stable characteristics of the intermediate states in the T cell differentiation. These dynamical features may help to direct the cells to correct lineages during development. Our findings provide general design principles for multistep cell linage transitions and new insights into the early T cell development. The network motifs containing a large family of topologies can be useful for analyzing diverse biological systems with multistep transitions.

The fundamental problem of nonlinear filtering theory is how to solve robust D-M-Z equation in real time and in memoryless manner. This paper describes a new real time algorithm which reduces the nonlinear filtering problem to off-line computations. Our algorithm gives convergent solutions in both pointwise sense and L/sup 2/ in case that the drift term and observation dynamic term have linear growths. The algorithm presented is slightly better than that given in our previous paper (2000).

Using the tri-hamiltonian splitting method, the authors of [Anco and Mobasheramini, Physica D, 355: 1--23, 2017] derived two U (1) -invariant nonlinear PDEs that arise from the hierarchy of the nonlinear Schrdinger equation and admit peakons ($ non-smooth\solitons $). In the present paper, these two peakon PDEs are generalized to a family of U (1) -invariant peakon PDEs parametrized by the real projective line U (1) . All equations in this family are shown to posses $ conservative\peakon\solutions $(whose Sobolev U (1) norm is time invariant). The Hamiltonian structure for the sector of conservative peakons is identified and the peakon ODEs are shown to be Hamiltonian with respect to several Poisson structures. It is shown that the resulting Hamilonian peakon flows in the case of the two peakon equations derived in [Anco and Mobasheramini, Physica D, 355: 1--23, 2017] form orthogonal families, while in general the Hamiltonian peakon flows for two different equations in the general family intersect at a fixed angle equal to the angle between two lines in U (1) parametrizing those two equations. Moreover, it is shown that inverse spectral methods allow one to solve explicitly the dynamics of conservative peakons using explicit solutions to a certain interpolation problem. The graphs of multipeakon solutions confirm the existence of multipeakon breathers as well as asymptotic formation of pairs of two peakon bound states in the non-periodic time domain.