arXiv subjects

Huaxiong Huang

Publications and source records attributed to Huaxiong Huang.

At least 37 records · Page 2Linked to original sources

arXiv2022

Mathematical Model for Chemical Reactions in Electrolyte Applied to Cytochrome $c$ Oxidase: an Electro-osmotic Approach

A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and dissipative functionals. The energy variation method is generalized to deal with open systems with inputs of charge, mass, and energy. The open systems can transform input energy of one type into output energy of another type. The generalized method is used to analyze the conversion of electrical current into proton flow by cytochrome c oxidase, an important enzyme in mitochondria that helps generate the 'energetic currency of life' ATP. The structure of the oxidase guides flows of current and mass that interact according to the energetic and dissipative functionals of the generalized theory. Kirchhoff's current law provides important coupling when the enzyme is in its natural setting in the mitochondrial membrane. The natural function of the enzyme is the result. Electron flows are converted into proton flows and gradients.

physics.chem-ph↗

arXiv2022

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.

physics.bio-ph↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2021

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↗

arXiv2020

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↗

arXiv2019

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↗

arXiv2019

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↗

arXiv2019

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↗

arXiv2019

What Current Flows Through a Resistor?

Our digital technology depends on mathematics to compute current flow and design its devices. Mathematics describes current flow by an idealization, Kirchhoff's current law. All the electrons that flow into a node flow out. This idealization describes real circuits only when stray capacitances are included in the circuit design. Motivated by Maxwell's equations, we propose that current in Kirchhoff's law be defined as \[{\varepsilon }_{\mathrm{0\ \ }}\frac{\mathrm{\partial }\boldsymbol{\mathrm{E}}}{\mathrm{\partial }t}\ \mathrm{+}\mathrm{\ }\mathrm{\ }\widetilde{\boldsymbol{\mathrm{J}}},\] the sum of (1) displacement current (2) the flux of charge associated with mass. The flux of charge associated with mass $\widetilde{\boldsymbol{\mathrm{J}}}$ includes, for example, the polarization of dielectrics as well as the movement of electrons. Kirchhoff's law becomes exact and universal when current is defined this way. This current is the source of the magnetic field; it is the source of $\boldsymbol{\mathrm{curl}}\boldsymbol{\mathrm{\ }}\boldsymbol{\mathrm{B}}$ in Maxwell's equations. Kirchoff's laws and Maxwell's equations can use the same definition of current.

physics.class-ph↗

arXiv2019

On the selectivity of KcsA potassium channel: asymptotic analysis and computation

Potassium (K$^+$) channels regulate the flux of K$^+$ ions through cell membranes and plays significant roles in many physiological functions. This work studies the KcsA potassium channel, including the selectivity and current-voltage (IV) relations. A modified Poisson-Nernst-Planck system is employed, which include the size effect by Bikerman model and solvation energy by Born model. The selectivity of KcsA for various ions (K$^+$, Na$^+$, Cl$^-$, Ca$^{2+}$ and Ba$^{2+}$) is studied analytically, and the profiles of concentrations and electric potential are provided. The selectivity is mainly influenced by permanent negative charges in filter of channel and the ion sizes. K$^+$ is always selected compared with Na$^+$ (or Cl$^-$), as smaller ion size of Na$^+$ causes larger solvation energy. There is a transition for selectivity among K$^+$ and divalent ions (Ca$^{2+}$ and Ba$^{2+}$), when negative charge in filter exceeds a critical value determined by ion size. This explains why divalent ions can block the KcsA channel. The profiles and IV relations are studied by analytical, numerical and hybrid methods, and are cross-validated. The results show the selectivity of the channel and also the saturation of IV curve. A simple strategy is given to compute IV relations analytically, as first approximation. The numerical method deals with general structure or parameters, but the limitations and difficulties of pure numerical simulation are also pointed out. The hybrid method provides IV relations most effectively for comparison. The reason for saturation of IV relation is illustrated, and the IV curve shows agreement with the profile and scale of experimental results.

physics.bio-ph↗

arXiv2018

Retirement spending and biological age

We solve a lifecycle model in which the consumer's chronological age does not move in lockstep with calendar time. Instead, biological age increases at a stochastic non-linear rate in time like a broken clock that might occasionally move backwards. In other words, biological age could actually decline. Our paper is inspired by the growing body of medical literature that has identified biomarkers which indicate how people age at different rates. This offers better estimates of expected remaining lifetime and future mortality rates. It isn't farfetched to argue that in the not-too-distant future personal age will be more closely associated with biological vs. calendar age. Thus, after introducing our stochastic mortality model we derive optimal consumption rates in a classic Yaari (1965) framework adjusted to our proper clock time. In addition to the normative implications of having access to biological age, our positive objective is to partially explain the cross-sectional heterogeneity in retirement spending rates at any given chronological age. In sum, we argue that neither biological nor chronological age alone is a sufficient statistic for making economic decisions. Rather, both ages are required to behave rationally.

q-fin.MF↗

arXiv2018

Electro-Neutral Models for dynamic Poisson-Nernst-Planck System: 2D Case

The Poisson-Nernst-Planck (PNP) system is a standard model for describing ion transport. In many applications, e.g., ions in biological tissues, the presence of thin boundary layers poses both modelling and computational challenges. In a previous paper, we derived simplified electro-neutral (EN) models in one dimensional space where the thin boundary layers are replaced by effective boundary conditions. In this paper, we extend our analysis to the two dimensional case where the EN model enjoys even greater advantages. First of all, it is much cheaper to solve the EN models numerically. Secondly, EN models are easier to deal with compared with the original PNP system, therefore it is also easier to derive macroscopic models for cellular structures using EN models. The multi-ion case with general boundary is considered, for a variety of boundary conditions including either Dirichlet or flux boundary conditions. Using systematic asymptotic analysis, we derive a variety of effective boundary conditions directly applicable to the EN system for the bulk region. To validate the EN models, numerical computations are carried out for both the EN and original PNP system, including the propagation of action potential for both myelinated and unmyelinated axons. Our results show that solving the EN models is much more efficient than the original PNP system.

physics.bio-ph↗

arXiv2018

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↗