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Yuanzhen Shao

Publications and source records attributed to Yuanzhen Shao.

At least 19 recordsLinked to original sources
arXiv2026

On calculating polar solvation energy of nonrigid proteins in the Poisson-Boltzmann theory

The Poisson-Boltzmann (PB) theory is a cornerstone of implicit solvent models for electrostatic analysis, and has found a great success in various biomolecular applications. However, in calculating polar solvation energy, one should consider that the structure of the protein changes upon transition from vacuum to water phases. To address this, here we report for the first time a generalized PB framework capable of accommodating nonrigid conformational changes without suffering from self-energy artifacts. For regularized PB models, in which the charge singularities are captured by the Green's functions, self-energies in the water and vacuum states will be analytically canceled. For non-regularized PB solvers, such as APBS and DelPhi, a simple thermodynamic cycle is proposed for nonrigid proteins by adding a Coulombic correction in vacuum. The generalized PB theory is validated using a perturbed two-atom system and a diverse set of proteins with different structures in vacuum and water, demonstrating its accuracy and robustness, regardless of the choice of sharp-interface and diffuse-interface PB models and different numerical solvers.

math.NA↗
arXiv2025

Degenerate parabolic $p$-Laplacian equations: existence, uniqueness and asymptotic behavior of solutions

In this paper we study the degenerate parabolic $p$-Laplacian,$ \partial_t u - v^{-1}{\rm div}(|\sqrt{Q} \nabla u|^{p-2} Q \nabla u)=0$, where the degeneracy is controlled by a matrix $Q$ and a weight $v$. With mild integrability assumptions on $Q$ and $v$, we prove the existence and uniqueness of solutions on any interval $[0,T]$. If we further assume the existence of a degenerate Sobolev inequality with gain, the degeneracy again controlled by $v$ and $Q$, then we can prove both finite time extinction and ultracontractive bounds. Moreover, we show that there is equivalence between the existence of ultracontractive bounds and the weighted Sobolev inequality.

math.AP↗
arXiv2024

Coriolis-driven fluid motion on spherical surfaces

We consider the motion of an incompressible viscous fluid on a sphere, incorporating the effects of the Coriolis force. We demonstrate that global solutions exist for any divergence-free initial condition with finite kinetic energy. Furthermore, we show that each solution converges at an exponential rate to a state that is aligned with the rotation of the sphere.

math.AP↗
arXiv2024

The Navier-Stokes equations on manifolds with boundary

We consider the motion of an incompressible viscous fluid on a compact Riemannian manifold $\sM$ with boundary. The motion on $\sM$ is modeled by the incompressible Navier-Stokes equations, and the fluid is subject to pure or partial slip boundary conditions of Navier type on $\partial\sM$. We establish existence and uniqueness of strong as well as weak (variational) solutions for initial data in critical spaces. Moreover, we show that the set of equilibria consists of Killing vector fields on $\sM$ that satisfy corresponding boundary conditions, and we prove that all equilibria are (locally) stable. In case $\sM$ is two-dimensional we show that solutions with divergence free initial condition in $L_2(\sM; T\sM)$ exist globally and converge to an equilibrium exponentially fast.

math.AP↗
arXiv2023

Modeling and analysis of ensemble average solvation energy and solute-solvent interfacial fluctuations

ariational implicit solvation models (VISM) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is an interface separating the solute and the solvent. However, traditional sharp-interface VISMs fall short in adequately representing the inherent randomness of the solute-solvent interface, a consequence of thermodynamic fluctuations within the solute-solvent system. Given that experimentally observable quantities are ensemble-averaged, the computation of the ensemble average solvation energy (EASE)-the averaged solvation energy across all thermodynamic microscopic states-emerges as a key metric for reflecting thermodynamic fluctuations during solvation processes. This study introduces a novel approach to calculating the EASE. We devise two diffuse-interface VISMs: one within the classic Poisson-Boltzmann (PB) framework and another within the framework of size-modified PB theory, accounting for the finite-size effects. The construction of these models relies on a new diffuse interface definition $u(x)$, which represents the probability of a point $x $ found in the solute phase among all microstates. Drawing upon principles of statistical mechanics and geometric measure theory, we rigorously demonstrate that the proposed models effectively capture EASE during the solvation process. Moreover, preliminary analyses indicate that the size-modified EASE functional surpasses its counterpart based on classic PB theory across various analytic aspects. Our work is the first step towards calculating EASE through the utilization of diffuse-interface VISM. energy by using diffuse-interface VISMs.

physics.bio-ph↗
arXiv2023

Strongly hyperbolic quasilinear systems revisited, with applications to relativistic fluid dynamics

We revisit the theory of first-order quasilinear systems with diagonalizable principal part and only real eigenvalues, what is commonly referred to as strongly hyperbolic systems. We provide a self-contained and simple proof of local well-posedness, in the Hadamard sense, of the Cauchy problem. Our regularity assumptions are very minimal. As an application, we apply our results to systems of ideal and viscous relativistic fluids, where the theory of strongly hyperbolic equations has been systematically used to study several systems of physical interest.

math.AP↗
arXiv2023

On a thermodynamically consistent model for magnetoviscoelastic fluids in 3D

We introduce a system of equations that models a non-isothermal magnetoviscoelastic fluid. We show that the model is thermodynamically consistent, and that the critical points of the entropy functional with prescribed energy correspond exactly with the equilibria of the system. The system is investigated in the framework of quasilinear parabolic systems and shown to be locally well-posed in an $L_p$-setting. Furthermore, we prove that constant equilibria are normally stable. In particular, we show that solutions that start close to a constant equilibrium exist globally and converge exponentially fast to a (possibly different) constant equilibrium. Finally, we establish that the negative entropy serves as a strict Lyapunov functional and we then show that every solution that is eventually bounded in the topology of the natural state space exists globally and converges to the set of equilibria.

math.AP↗
arXiv2022

The fractional porous medium equation on manifolds with conical singularities II

This is the second of a series of two papers which studies the fractional porous medium equation, $\partial_t u +(-Δ)^σ(|u|^{m-1}u )=0 $ with $m>0$ and $σ\in (0,1]$, posed on a Riemannian manifold with isolated conical singularities. The first aim of the article is to derive some useful properties for the Mellin-Sobolev spaces including the Rellich-Kondrachov Theorem and Sobolev-Poincaré, Nash and Super Poincaré type inequalities. The second part of the article is devoted to the study the Markovian extensions of the conical Laplacian operator and its fractional powers. Then based on the obtained results, we establish existence and uniqueness of a global strong solution for $L_\infty-$initial data and all $m>0$. We further investigate a number of properties of the solutions, including comparison principle, $L_p-$contraction and conservation of mass. Our approach is quite general and thus is applicable to a variety of similar problems on manifolds with more general singularities.

math.AP↗
arXiv2022

Well-posedness for magnetoviscoelastic fluids in 3D

We show that the system of equations describing a magnetoviscoelastic fluid in three dimensions can be cast as a quasilinear parabolic system. Using the theory of maximal $L_p$-regularity, we establish existence and uniqueness of local strong solutions and we show that each solution is smooth (in fact analytic) in space and time. Moreover, we give a complete characterization of the set of equilibria and show that solutions that start out close to a constant equilibrium exist globally and converge to a (possibly different) constant equilibrium. Finally, we show that every solution that is eventually bounded in the topology of the state space exists globally and converges to the set of equilibria.

math.AP↗
arXiv2022

A new approach to constrained total variation solvation models and the study of solute-solvent interface profiles

In the past decade, variational implicit solvation models (VISM) have achieved great success in solvation energy predictions. However, all existing VISMs in literature lack the uniqueness of an energy minimizing solute-solvent interface and thus prevent us from studying many important properties of the interface profile. To overcome this difficulty, we introduce a new constrained VISM and conduct a rigorous analysis of the model. Existence, uniqueness and regularity of the energy minimizing interface has been studied. A necessary condition for the formation of a sharp solute-solvent interface has been derived. Moreover, we develop a novel approach to the variational analysis of the constrained model, which provides a complete answer to a question in our previous work [55]. Model validation and numerical implementation have been demonstrated by using several common biomolecular modeling tasks. Numerical simulations show that the solvation energies calculated from our new model match the experimental data very well.

math.AP↗
arXiv2022

The fractional porous medium equation on manifolds with conical singularities I

This is the first of a series of two papers which studies the fractional porous medium equation on a Riemannian manifold with isolated conical singularities. In this article, we show $R$-sectoriality for the fractional powers of possibly non-invertible $R$-sectorial operators. Applications concern existence, uniqueness and maximal $L^{q}$-regularity results for solutions of the fractional porous medium equation on manifolds with conical singularities. Space asymptotic behavior of the solutions close to the singularities is provided and its relation to the local geometry is established. Our method extends the freezing-of-coefficients method to the case of non-local operators that are expressed as linear combinations of terms in the form of a product of a function and a fractional power of a local operator.

math.AP↗
arXiv2021

Functional Inequalities involving Nonlocal Operators on Complete Riemannian Manifolds and Their Applications to The Fractional Porous Medium Equation

The objective of this paper is twofold. First, we conduct a careful study of various functional inequalities involving the fractional Laplacian operators, including nonlocal Sobolev-Poincaré, Nash, Super Poincaré and logarithmic Sobolev type inequalities, on complete Riemannian manifolds satisfying some mild geometric assumptions. Second, based on the derived nonlocal functional inequalities, we analyze the asymptotic behavior of the solution to the fractional porous medium equation, $\partial_t u +(-Δ)^σ(|u|^{m-1}u )=0 $ with $m>0$ and $σ\in (0,1)$. In addition, we establish the global well-posedness of the equation on an arbitrary complete Riemannian manifold.

math.AP↗
arXiv2019

Local well-posedness in Sobolev spaces for first-order conformal causal relativistic viscous hydrodynamics

In this manuscript, we study the theory of conformal relativistic viscous hydrodynamics introduced in arXiv:1708.06255, which provided a causal and stable first-order theory of relativistic fluids with viscosity. The local well-posedness of its equations of motion has been previously established in Gevrey spaces. Here, we improve this result by proving local well-posedness in Sobolev spaces.

math.AP↗
arXiv2019

The surface diffusion and the Willmore flow for uniformly regular hypersurfaces

We consider the surface diffusion and Willmore flows acting on a general class of (possibly non-compact) hypersurfaces parameterized over a uniformly regular reference manifold possessing a tubular neighborhood with uniform radius. The surface diffusion and Willmore flows each give rise to a fourth-order quasilinear parabolic equation with nonlinear terms satisfying a specific singular structure. We establish well-posedness of both flows for initial surfaces that are $C^{1+α}$-regular and parameterized over a uniformly regular hypersurface. For the Willmore flow, we also show long-term existence for initial surfaces which are $C^{1+α}$-close to a sphere, and we prove that these solutions become spherical as time goes to infinity.

math.AP↗
arXiv2017

The harmonic map heat flow on conic manifolds

In this article, we study the the harmonic map heat flow from a manifold with conic singularities to a closed manifold. In particular, we have proved the short time existence and uniqueness of solutions as well as the existence of global solutions into manifolds with nonpositive sectional curvature. These results are established in virtue of the maximal regularity theory on manifolds with conic singularities.

math.AP↗
arXiv2017

The Yamabe flow on incomplete manifolds

This article is concerned with developing an analytic theory for second order nonlinear parabolic equations on singular manifolds. Existence and uniqueness of solutions in an Lp-framework is established by maximal regularity tools. These techniques are applied to the Yamabe flow. It is proven that the Yamabe flow admits a unique local solution within a class of incomplete initial metrics.

math.AP↗
arXiv2016

Wellposedness of a nonlocal nonlinear diffusion equation of image processing

Existence and uniqueness are established for a degenerate regularization of the well-known Perona-Malik equation proposed by the first author for non-smooth initial data. The results heavily rely on the choice of appropriate functional setting inspired by a recent approach to degenerate parabolic equations via so-called singular Riemannian manifolds introduced by Herbert Amann.

math.AP↗