Riemannian optimization using three different metrics for Hermitian PSD fixed-rank constraints: an extended version

We consider smooth optimization problems with a Hermitian positive semi-definite fixed-rank constraint, where a quotient geometry with three Riemannian metrics $g^i(\cdot, \cdot)$ $(i=1,2,3)$ is used to represent this constraint. By taking the nonlinear conjugate gradient method (CG) as an example, we show that CG on the quotient geometry with metric $g^1$ is equivalent to CG on the factor-based optimization framework, which is often called the Burer--Monteiro approach. We also show that CG on the quotient geometry with metric $g^3$ is equivalent to CG on the commonly-used embedded geometry. We call two CG methods equivalent if they produce an identical sequence of iterates $\{X_k\}$. In addition, we show that if the limit point of the sequence $\{X_k\}$ generated by an algorithm has lower rank, that is $X_k\in \mathbb C^{n\times n}, k = 1, 2, \ldots$ has rank $p$ and the limit point $X_*$ has rank $r < p$, then the condition number of the Riemannian Hessian with metric $g^1$ can be unbounded, but those of the other two metrics stay bounded. Numerical experiments show that the Burer--Monteiro CG method has slower local convergence rate if the limit point has a reduced rank, compared to CG on the quotient geometry under the other two metrics. This slower convergence rate can thus be attributed to the large condition number of the Hessian near a minimizer

A Bubble Model for the Gating of Kv Channels

Voltage-gated Kv channels play fundamental roles in many biological processes, such as the generation of the action potential. The gating mechanism of Kv channels is characterized experimentally by single-channel recordings and ensemble properties of the channel currents. In this work, we propose a bubble model coupled with a Poisson-Nernst-Planck (PNP) system to capture the key characteristics, particularly the delay in the opening of channels. The coupled PNP system is solved numerically by a finite-difference method and the solution is compared with an analytical approximation. We hypothesize that the stochastic behaviour of the gating phenomenon is due to randomness of the bubble and channel sizes. The predicted ensemble average of the currents under various applied voltages across the channels is consistent with experimental observations, and the Cole-Moore delay is captured by varying the holding potential

Micro-Macro Modeling of Polymeric Fluids and Shear-Induced Microscopic Behaviors

This article delves into the micro-macro modeling of polymeric fluids, considering various microscopic potential energies, including the classical Hookean potential, as well as newly proposed modified Morse and Elastic-plastic potentials. These proposed potentials encompass microscopic-scale bond-breaking processes. The development of a thermodynamically consistent micro-macro model is revisited, employing the energy variational method. To validate the model's predictions, we conduct numerical simulations utilizing a deterministic particle-FEM method. Our numerical findings shed light on the distinct behaviors exhibited by polymer chains at the micro-scale in comparison to the macro-scale velocity and induced shear stresses of fluids under shear flow. Notably, we observe that polymer elongation, rotation, and bond breaking contribute to the zero polymer-induced stress in the micro-macro model when employing Morse and Elastic-plastic potentials. Furthermore, at high shear rates, polymer rotation is found to induce shear-thinning behavior in the model employing the classical Hookean potential

A phase field model for mass transport with semi-permeable interfaces

In this paper, a thermal-dynamical consistent model for mass transfer across permeable moving interfaces is proposed by using the energy variation method. We consider a restricted diffusion problem where the flux across the interface depends on its conductance and the difference of the concentration on each side. The diffusive interface phase-field framework used here has several advantages over the sharp interface method. First of all, explicit tracking of the interface is no longer necessary. Secondly, the interfacial condition can be incorporated with a variable diffusion coefficient. A detailed asymptotic analysis confirms the diffusive interface model converges to the existing sharp interface model as the interface thickness goes to zero. A decoupled energy stable numerical scheme is developed to solve this system efficiently. Numerical simulations first illustrate the consistency of theoretical results on the sharp interface limit. Then a convergence study and energy decay test are conducted to ensure the efficiency and stability of the numerical scheme. To illustrate the effectiveness of our phase-field approach, several examples are provided, including a study of a two-phase mass transfer problem where drops with deformable interfaces are suspended in a moving fluid.Comment: 20 pages, 15 figure

An energy stable C⁰ finite element scheme for a quasi-incompressible phase-field model of moving contact line with variable density

In this paper, we focus on modeling and simulation of two-phase flow with moving contact lines and variable density. A thermodynamically consistent phase-field model with General Navier Boundary Condition is developed based on the concept of quasi-incompressibility and the energy variational method. Then a mass conserving and energy stable C0 finite element scheme is developed to solve the PDE system. Various numerical simulation results show that the proposed schemes are mass conservative, energy stable and the 2nd order for P1 element and 3rd order for P2 element convergence rate in the sense of L2 norm