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Shixin Xu

Publications and source records attributed to Shixin Xu.

At least 55 records · Page 3Linked to original sources

Neural-PDE: A RNN based neural network for solving time dependent PDEs

Partial differential equations (PDEs) play a crucial role in studying a vast number of problems in science and engineering. Numerically solving nonlinear and/or high-dimensional PDEs is often a challenging task. Inspired by the traditional finite difference and finite elements methods and emerging advancements in machine learning, we propose a sequence deep learning framework called Neural-PDE, which allows to automatically learn governing rules of any time-dependent PDE system from existing data by using a bidirectional LSTM encoder, and predict the next n time steps data. One critical feature of our proposed framework is that the Neural-PDE is able to simultaneously learn and simulate the multiscale variables.We test the Neural-PDE by a range of examples from one-dimensional PDEs to a high-dimensional and nonlinear complex fluids model. The results show that the Neural-PDE is capable of learning the initial conditions, boundary conditions and differential operators without the knowledge of the specific form of a PDE system.In our experiments the Neural-PDE can efficiently extract the dynamics within 20 epochs training, and produces accurate predictions. Furthermore, unlike the traditional machine learning approaches in learning PDE such as CNN and MLP which require vast parameters for model precision, Neural-PDE shares parameters across all time steps, thus considerably reduces the computational complexity and leads to a fast learning algorithm.

math.NA↗

A Level Set Method for the Simulation of Moving Contact Lines in Three Dimensions

We propose an efficient numerical method for the simulation of multi-phase flows with moving contact lines in three dimensions. The mathematical model consists of the incompressible Navier-Stokes equations for the two immiscible fluids with the standard interface conditions, the Navier slip condition along the solid wall, and a contact angle condition which relates the dynamic contact angle to the normal velocity of the contact line (Ren et al. (2010) \cite{Ren10}). In the numerical method, the governing equations for the fluid dynamics are coupled with an advection equation for a level-set function. The latter models the dynamics of the fluid interface. Following the standard practice, the interface conditions are taken into account by introducing a singular force on the interface in the momentum equation. This results in a single set of governing equations in the whole fluid domain. Similar to the treatment of the interface conditions, the contact angle condition is imposed by introducing a singular force, which acts in the normal direction of the contact line, into the Navier slip condition. The new boundary condition, which unifies the Navier slip condition and the contact angle condition, is imposed along the solid wall. The model is solved using the finite difference method. Numerical results, including a convergence study, are presented for the spreading of a droplet on both homogeneous and inhomogeneous solid walls, as well as the dynamics of a droplet on an inclined plate under gravity.

physics.flu-dyn↗

Multi-objective optimization and explanation for stroke risk assessment in Shanxi province

Stroke is the top leading causes of death in China (Zhou et al. The Lancet 2019). A dataset from Shanxi Province is used to identify the risk of each patient's at four states low/medium/high/attack and provide the state transition tendency through a SHAP DeepExplainer. To improve the accuracy on an imbalance sample set, the Quadratic Interactive Deep Neural Network (QIDNN) model is first proposed by flexible selecting and appending of quadratic interactive features. The experimental results showed that the QIDNN model with 7 interactive features achieve the state-of-art accuracy $83.25\%$. Blood pressure, physical inactivity, smoking, weight and total cholesterol are the top five important features. Then, for the sake of high recall on the most urgent state, attack state, the stroke occurrence prediction is taken as an auxiliary objective to benefit from multi-objective optimization. The prediction accuracy was promoted, meanwhile the recall of the attack state was improved by $24.9\%$ (to $84.83\%$) compared to QIDNN (from $67.93\%$) with same features. The prediction model and analysis tool in this paper not only gave the theoretical optimized prediction method, but also provided the attribution explanation of risk states and transition direction of each patient, which provided a favorable tool for doctors to analyze and diagnose the disease.

cs.LG↗

Membranes in Optic Nerve Models

Membranes are present in all cells and tissues. Mathematical models of cells and tissues need a compact mathematical description of membranes with a resolution of about 1 nm. Membranes isolate cells because ions have difficulty penetrating the dielectric barrier they create. Here we introduce a dielectric mathematical membrane condition to replace a condition that did not include dielectric properties. Our mathematical membrane condition includes a dielectric lipid bilayer punctured by channels that conduct ions selectively.

math.DS↗

Analysis and classification of main risk factors causing stroke in Shanxi Province

In China, stroke is the first leading cause of death in recent years. It is a major cause of long-term physical and cognitive impairment, which bring great pressure on the National Public Health System. Evaluation of the risk of getting stroke is important for the prevention and treatment of stroke in China. A data set with 2000 hospitalized stroke patients in 2018 and 27583 residents during the year 2017 to 2020 is analyzed in this study. Due to data incompleteness, inconsistency, and non-structured formats, missing values in the raw data are filled with -1 as an abnormal class. With the cleaned features, three models on risk levels of getting stroke are built by using machine learning methods. The importance of "8+2" factors from China National Stroke Prevention Project (CSPP) is evaluated via decision tree and random forest models. Except for "8+2" factors the importance of features and SHAP1 values for lifestyle information, demographic information, and medical measurement are evaluated and ranked via a random forest model. Furthermore, a logistic regression model is applied to evaluate the probability of getting stroke for different risk levels. Based on the census data in both communities and hospitals from Shanxi Province, we investigate different risk factors of getting stroke and their ranking with interpretable machine learning models. The results show that Hypertension (Systolic blood pressure, Diastolic blood pressure), Physical Inactivity (Lack of sports), and Overweight (BMI) are ranked as the top three high-risk factors of getting stroke in Shanxi province. The probability of getting stroke for a person can also be predicted via our machine learning model.

cs.LG↗

A Tridomain Model for Potassium Clearance in Optic Nerve of Necturus

The accumulation of potassium in the narrow space outside nerve cells is a classical subject of biophysics that has received much attention recently. It may be involved in potassium accumulation \textcolor{black}{including} spreading depression, perhaps migraine and some kinds of epilepsy, even (speculatively) learning. Quantitative analysis is likely to help evaluate the role of potassium clearance from the extracellular space after a train of action potentials. Clearance involves three structures that extend down the length of the nerve: glia, extracellular space, and axon and so need to be described as systems distributed in space in the tradition used for electrical potential in the `cable equations' of nerve since the work of Hodgkin in 1937. A three-compartment model is proposed here for the optic nerve and is used to study the accumulation of potassium and its clearance. The model allows the convection, diffusion, and electrical migration of water and ions. We depend on the data of Orkand et al to ensure the relevance of our model and align its parameters with the anatomy and properties of membranes, channels, and transporters: our model fits their experimental data quite well. The aligned model shows that glia has an important role in buffering potassium, as expected. The model shows that potassium is cleared mostly by convective flow through the syncytia of glia driven by osmotic pressure differences. A simplified model might be possible, but it must involve flow down the length of the optic nerve. It is easy for compartment models to neglect this flow. Our model can be used for structures quite different from the optic nerve that might have different distributions of channels and transporters in its three compartments. It can be generalized to include a fourth (distributed) compartment representing blood vessels to deal with the glymphatic flow into the circulatory system.

physics.bio-ph↗

Optic Nerve Microcirculation: Fluid Flow and Electrodiffusion

Complex fluids flow in complex ways in complex structures. Transport of water and various organic and inorganic molecules in the central nervous system are important in a wide range of biological and medical processes [C. Nicholson, and S. Hrabětová, Biophysical Journal, 113(10), 2133(2017)]. However, the exact driving mechanisms are often not known. In this paper, we investigate flows induced by action potentials in an optic nerve as a prototype of the central nervous system (CNS). Different from traditional fluid dynamics problems, flows in biological tissues such as the CNS are coupled with ion transport. It is driven by osmosis created by concentration gradient of ionic solutions, which in term influence the transport of ions. Our mathematical model is based on the known structural and biophysical properties of the experimental system used by the Harvard group Orkand et al [R.K. Orkand, J.G. Nicholls, S.W. Kuffler, Journal of Neurophysiology, 29(4), 788(1966)]. Asymptotic analysis and numerical computation show the significant role of water in convective ion transport. The full model (including water) and the electrodiffusion model (excluding water) are compared in detail to reveal an interesting interplay between water and ion transport. In the full model, convection due to water flow dominates inside the glial domain. This water flow in the glia contributes significantly to the spatial buffering of potassium in the extracellular space. Convection in the extracellular domain does not contribute significantly to spatial buffering. Electrodiffusion is the dominant mechanism for flows confined to the extracellular domain.

physics.bio-ph↗

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.

math.NA↗

Homogenization Theory of Ion Transportation in Multicellular Tissue

Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like smooth muscles on the vessel walls, could be treated as periodic bi-domain structures, which consist of intracellular space and extracellular space with semipermeable membranes in between. With the aid of two-scale homogenization theory, macro-scale models are proposed based on an electro-neutral (EN) microscale model with nonlinear interface conditions, where membranes are treated as combinations of capacitors and resistors. The connectivity of intracellular space is also taken into consideration. If the intracellular space is fully connected and forms a syncytium, then the macroscale model is a bidomain nonlinear coupled partial differential equations system. Otherwise, when the intracellular cells are not connected, the macroscale model for intracellular space is an ordinary differential system with source/sink terms from the connected extracellular space.

math.AP↗

An Energy Stable C0 Finite Element Scheme for A Phase-Field Model of Vesicle Motion and Deformation

A thermodynamically consistent phase-field model is introduced for simulating motion and shape transformation of vesicles under flow conditions. In particular, a general slip boundary condition is used to describe the interaction between vesicles and the wall of the fluid domain. A second-order accurate in both space and time C0 finite element method is proposed to solve the model governing equations. Various numerical tests confirm the convergence, energy stability, and conservation of mass and surface area of cells of the proposed scheme. Vesicles with different mechanical properties are also used to explain the pathological risk for patients with sickle cell disease.

math.NA↗

Numerical Method for Parameter Inference of Nonlinear ODEs with Partial Observations

Parameter inference of dynamical systems is a challenging task faced by many researchers and practitioners across various fields. In many applications, it is common that only limited variables are observable. In this paper, we propose a method for parameter inference of a system of nonlinear coupled ODEs with partial observations. Our method combines fast Gaussian process based gradient matching (FGPGM) and deterministic optimization algorithms. By using initial values obtained by Bayesian steps with low sampling numbers, our deterministic optimization algorithm is both accurate and efficient.

stat.ME↗

An energy stable $C^0$ 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.

math.NA↗

A Bidomain Model for Lens Microcirculation

There exists a large body of research on the lens of mammalian eye over the past several decades. The objective of the current work is to provide a link between the most recent computational models to some of the pioneering work in the 1970s and 80s. We introduce a general non-electro-neutral model to study the microcirculation in lens of eyes. It describes the steady state relationships among ion fluxes, water flow and electric field inside cells, and in the narrow extracellular spaces between cells in the lens. Using asymptotic analysis, we derive a simplified model based on physiological data and compare our results with those in the literature. We show that our simplified model can be reduced further to the first generation models while our full model is consistent with the most recent computational models. In addition, our simplified model captures the main features of the full model. Our results serve as a useful link intermediate between the computational models and the first generation analytical models.

q-bio.TO↗

Osmosis through a Semi-permeable Membrane: a Consistent Approach to Interactions

The movement of ionic solutions is an essential part of biology and technology. Fluidics, from nano- to micro- to microfluidics, is a burgeoning area of technology which is all about the movement of ionic solutions, on various scales. Many cells, tissues, and organs of animals and plants depend on osmosis, as the movement of fluids is called in biology. Indeed, the movement of fluids through channel proteins (that have a hole down their middle) is fluidics on an atomic scale. Ionic fluids are complex fluids, with energy stored in many ways. Ionic fluids flow driven by gradients of concentration, chemical and electrical potential, and hydrostatic pressure. Each flow is classically described by its own field theory, independent of the others, but of course, in reality every gradient drives every kind of flow to a varying extent. Combining field equations is tricky and so the theory of complex fluids derives the equations, rather than assumes their interactions. When field equations are derived, rather than assumed, their variables are consistent. That is to say all variables satisfy all equations under all conditions with one set of parameters. Here we treat a classical osmotic cell in this spirit, using a sharp interface method to derive boundary conditions consistent with all flows and fields. We allow volume to change with concentration, since changes of volume are a property of ionic solutions known to all who make them in the laboratory. We consider flexible and inflexible membranes. We show how to combine the energetics of the membrane with the energetics of the surrounding complex fluids. The results seem general but need application to specific situations of technological, biological and experimental importance before the consequences of consistency can be understood.

q-bio.QM↗

Behavior of different numerical schemes for population genetic drift problems

In this paper, we focus on numerical methods for the genetic drift problems, which is governed by a degenerated convection-dominated parabolic equation. Due to the degeneration and convection, Dirac singularities will always be developed at boundary points as time evolves. In order to find a \emph{complete solution} which should keep the conservation of total probability and expectation, three different schemes based on finite volume methods are used to solve the equation numerically: one is a upwind scheme, the other two are different central schemes. We observed that all the methods are stable and can keep the total probability, but have totally different long-time behaviors concerning with the conservation of expectation. We prove that any extra infinitesimal diffusion leads to a same artificial steady state. So upwind scheme does not work due to its intrinsic numerical viscosity. We find one of the central schemes introduces a numerical viscosity term too, which is beyond the common understanding in the convection-diffusion community. Careful analysis is presented to prove that the other central scheme does work. Our study shows that the numerical methods should be carefully chosen and any method with intrinsic numerical viscosity must be avoided.

math.NA↗

The Poisson Boltzmann equation and the charge separation phenomenon at the silica-water interface: A holistic approach

The Poisson Boltzmann equation is known for its success in describing the Debye layer that arises from the charge separation phenomenon at the silica/water interface. However, by treating only the mobile ionic charges in the liquid, the Poisson Boltzmann equation accounts for only half of the electrical double layer, with the other half, the surface charge layer, being beyond its computational domain. In this work, we take a holistic approach to the charge separation phenomenon at the silica/water interface by treating, within a single computational domain, the electrical double layer that comprises both the mobile ions in the liquid and the surface charge density. The Poisson Nernst Planck equations are used as the rigorous basis for our methodology. The holistic approach has the advantage of being able to predict surface charge variations that arise either from the addition of salt and acid to the liquid, or from the decrease of the liquid channel width to below twice the Debye length. As the electrical double layer must be overall neutral, we use this constraint to derive both the form of the static limit of the Poisson Nernst Planck equations, as well as a global chemical potential that replaces the classical zeta potential as the boundary value for the PB equation, which can be re-derived from our formalism. We present several predictions of our theory that are beyond the framework of the PB equation alone, e.g., the surface capacitance and the so-called pK and pL values, the isoelectronic point at which the surface charge layer is neutralized, and the appearance of a Donnan potential that arises from the formation of an electrical double layer at the inlet regions of a nano-channel connected to the bulk reservoir. All theory predictions are shown to be in good agreement with the experimental observations.

cond-mat.soft↗

An Energetic Variational Approach for ion transport

The transport and distribution of charged particles are crucial in the study of many physical and biological problems. In this paper, we employ an Energy Variational Approach to derive the coupled Poisson-Nernst-Planck-Navier-Stokes system. All physics is included in the choices of corresponding energy law and kinematic transport of particles. The variational derivations give the coupled force balance equations in a unique and deterministic fashion. We also discuss the situations with different types of boundary conditions. Finally, we show that the Onsager's relation holds for the electrokinetics, near the initial time of a step function applied field.

physics.flu-dyn↗