Electrothermal equivalent three-dimensional Finite Element Model of a single neuron

Objective: We propose a novel approach for modelling the inter-dependence of electrical and mechanical phenomena in nervous cells, by using electro-thermal equivalences in finite element (FE) analysis so that existing thermo-mechanical tools can be applied. Methods: First, the equivalence between electrical and thermal properties of the nerve materials is established, and results of a pure heat conduction analysis performed in Abaqus CAE Software 6.13-3 are validated with analytical solutions for a range of steady and transient conditions. This validation includes the definition of equivalent active membrane properties that enable prediction of the action potential. Then, as a step towards fully coupled models, electromechanical coupling is implemented through the definition of equivalent piezoelectric properties of the nerve membrane using the thermal expansion coefficient, enabling prediction of the mechanical response of the nerve to the action potential. Results: Results of the coupled electro-mechanical model are validated with previously published experimental results of deformation for the squid giant axon, crab nerve fibre and garfish olfactory nerve fibre. Conclusion: A simplified coupled electro-mechanical modelling approach is established through an electro-thermal equivalent FE model of a nervous cell for biomedical applications. Significance: One of the key findings is the mechanical characterization of the neural activity in a coupled electro-mechanical domain, which provides insights into the electromechanical behaviour of nervous cells, such as thinning of the membrane. This is a first step towards modelling 3D electromechanical alteration induced by trauma at nerve bundle, tissue and organ levels

Efficient Implicit Runge-Kutta Methods for Fast-Responding Ligand-Gated Neuroreceptor Kinetic Models

Neurophysiological models of the brain typically utilize systems of ordinary differential equations to simulate single-cell electrodynamics. To accurately emulate neurological treatments and their physiological effects on neurodegenerative disease, models that incorporate biologically-inspired mechanisms, such as neurotransmitter signalling, are necessary. Additionally, applications that examine populations of neurons, such as multiscale models, can demand solving hundreds of millions of these systems at each simulation time step. Therefore, robust numerical solvers for biologically-inspired neuron models are vital. To address this requirement, we evaluate the numerical accuracy and computational efficiency of three L-stable implicit Runge-Kutta methods when solving kinetic models of the ligand-gated glutamate and gamma-aminobutyric acid (GABA) neurotransmitter receptors. Efficient implementations of each numerical method are discussed, and numerous performance metrics including accuracy, simulation time steps, execution speeds, Jacobian calculations, and LU factorizations are evaluated to identify appropriate strategies for solving these models. Comparisons to popular explicit methods are presented and highlight the advantages of the implicit methods. In addition, we show a machine-code compiled implicit Runge-Kutta method implementation that possesses exceptional accuracy and superior computational efficiency

Thermal Effects in Atomic and Molecular Polarizabilities with Path Integral Monte Carlo

Väitöskirja käsittelee polarisoituvuutta ja erilaisia keinoja sen laskemiseksi polkuintegraali–Monte Carlo -menetelmällä (PIMC). Polarisoituvuus on kvanttimekaaninen suure, joka vastaa sähköistä suskeptibiliteettiä: se kuvaa atomien ja molekyylien vastetta sähkökenttään. Staattiset ja dynaamiset multipoli-polarisoituvuudet ovatkin yksiä tärkeimmistä elektronien vasteominaisuuksista ja näin ollen monikäyttöisiä parametrejä fysikaalisessa mallinnuksessa. Polarisoituvuuksien äärimmäisen tarkka laskeminen on kuitenkin haasteellista. Väitöskirjassa keskitytään siksi muutamaan erityiseen ongelmaan: tarkkaan monen kappaleen korrelaatiokuvaukseen, ei-adiabaattisiin efekteihin sekä lämpötilan vaikutuksiin.Tässä työssä polarisoituvuuksien laskemista tarkastellaan ei-relativistisesti Feynmanin polkuintegraalien ja termisten tiheysmatriisien avulla. Sähkökentän ja sähköisten multipolien välinen vuorovaikutus kytketään kausaalisiin korrelaatiofunktioihin sekä epälineaarisen vasteen teoriaan. Uusi tieteellinen ansio muodostuu muutamasta erilaisesta keinosta määrittää polarisoituvuus PIMC-laskuista: äärellisen kentän simulointi, staattiset kenttä-derivaatan estimaattorit, sekä imaginääriajan korrelaatiofunktioiden analyyttinen jatkaminen. Vaadittu Matsubara-taajuuksien analyyttinen jatkaminen on yleisesti esiintyvä mutta huonosti määritelty numeerinen ongelma, jota lähestytään tässä työssä maksimientropiamenetelmällä.Tärkeimmät laskennalliset tulokset ovat seuraavien yhden tai kahden elektronin systeemien polarisoituvuudet ja hyperpolarisoituvuudet: H, H2+, H2, H3+, HD+, He, He+, HeH+, Li+, Be2+, Ps, PsH, ja Ps2. Born–Oppenheimer-approksimaatiossa (BO) lasketut referenssitulokset vastaavat tunnettuja kirjallisuuden arvoja ja monessa tapauksessa myös täydentävät niitä. BO-approksimaation ulkopuolelta voidaan osoittaa mm. rovibraatiosta johtuvia heikkoja sekä voimakkaita lämpötilaefektejä. Muut tulokset käsittävät multipoli-spektrejä, dynaamisia polarisoituvuuksia sekä van der Waals-vakioita. Simulaatioiden kvanttimekaaninen kuvaus monen kappaleen korrelaatioista sekä elektronien ja ytimien ei-ediabaattisesta kytkennästä on poikkeuksellisen tarkka.This Thesis is a review of polarizability and different means to estimate it from pathintegral Monte Carlo (PIMC) simulations. Polarizability is the quantum mechanical equivalent of electric susceptibility: it describes the electric field response of atoms and molecules. The static and dynamic multipole polarizabilies are, arguably, the most important electronic response properties and multipurpose parameters for physical modeling. Computing them from first principles is challenging in many ways, and in this Thesis we focus on a few particular aspects: exact many-body correlations, nonadiabatic effects and thermal coupling. The Thesis contains an introduction to polarizability in the framework of nonrelativistic Feynman path integrals and thermal density matrices. The electric field interactions due to electric multipoles is associated with causal time-correlation functions and nonlinear response theory. The original scientific contribution manifests in various strategies to obtain the polarizabilities from PIMC simulations: we demonstrate finite-field simulations, static field-derivative estimators, and analytic continuation of imaginarytime correlation functions. The required analytic continuation of Matsubara frequencies is a common but ill-posed numerical challenge, which we approach with the Maximum Entropy method. For data, we provide the most important polarizabilities and hyperpolarizabilities of several one- or two-electron systems: H, H2+, H2, H3+, HD+, He, He+, HeH+, Li+, Be2+, Ps, PsH, and Ps2. Our benchmark simulations within the Born–Oppenheimer approximation (BO) agree with the available literature and complement it in many cases. Beyond BO, we are able to demonstrate weak and strong thermal effects due to, e.g., rovibrational coupling. We also estimate the first-order multipole spectra, dynamic polarizabilities and van der Waals coefficients. The simulations show unprecedented accuracy in terms of exact many-body correlations and fully nonadiabatic coupling of the electronic and nuclear quantum effects