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Funding Information: This study was supported by National Institutes of Health (Grant Nos. NIBIB RO1 EB022889, NIMH RO1 MH106174). Publisher Copyright: © 2021, The Author(s). Auditory evoked fields (AEFs) are commonly studied, yet their underlying neural mechanisms remain poorly understood. Here, we used the biophysical modelling software Human Neocortical Neurosolver (HNN) whose foundation is a canonical neocortical circuit model to interpret the cell and network mechanisms contributing to macroscale AEFs elicited by a simple tone, measured with magnetoencephalography. We found that AEFs can be reproduced by activating the neocortical circuit through a layer specific sequence of feedforward and feedback excitatory synaptic drives, similar to prior simulation of somatosensory evoked responses, supporting the notion that basic structures and activation patterns are preserved across sensory regions. We also applied the modeling framework to develop and test predictions on neural mechanisms underlying AEF differences in the left and right hemispheres, as well as in hemispheres contralateral and ipsilateral to the presentation of the auditory stimulus. We found that increasing the strength of the excitatory synaptic cortical feedback inputs to supragranular layers simulates the commonly observed right hemisphere dominance, while decreasing the input latencies and simultaneously increasing the number of cells contributing to the signal accounted for the contralateral dominance. These results provide a direct link between human data and prior animal studies and lay the foundation for future translational research examining the mechanisms underlying alteration in this fundamental biomarker of auditory processing in healthy cognition and neuropathology.

Broader use of bio-based fibres in packaging becomes possible when the mechanical properties of fibre materials exceed those of conventional paperboard. Hot-pressing provides an efficient method to improve both the wet and dry strength of lignin-containing paper webs. Here we study varied pressing conditions for webs formed with thermomechanical pulp (TMP). The results are compared against similar data for a wide range of other fibre types. In addition to standard strength and structural measurements, we characterise the induced structural changes with X-ray microtomography and scanning electron microscopy. The wet strength generally increases monotonously up to a very high pressing temperature of 270 °C. The stronger bonding of wet fibres can be explained by the inter-diffusion of lignin macromolecules with an activation energy around 26 kJ mol−1 after lignin softening. The associated exponential acceleration of diffusion with temperature dominates over other factors such as process dynamics or final material density in setting wet strength. The optimum pressing temperature for dry strength is generally lower, around 200 °C, beyond which hemicellulose degradation begins. By varying the solids content prior to hot-pressing for the TMP sheets, the highest wet strength is achieved for the completely dry web, while no strong correlation was observed for the dry strength.

The transport of molecules inside cells is a complex process, the characterization of which is important to gain full understanding of cellular processes. Understanding of intracellular transport is also important for medical applications, for example when analyzing transport of medicine inside cells. The intracellular environment is very complex, and at least the most crucial parts of this complexity must be accounted for to solve transport problems in cells. In this thesis the results of studies in modeling intracellular transport are presented. The aim of the work was to model intracellular transport of proteins and viral capsids in realistic cell environments. To this end, microscopic methods were used to image cellular structures, which were then digitally reconstructed and used as an environment for modeling particle transport in numerical simulations.

One of the central tasks of investigation of dynamical systems is the problem of analysis of the steady (limiting) behavior of the system after the completion of transient processes, i.e., the problem of localization and analysis of attractors (bounded sets of states of the system to which the system tends after transient processes from close initial states). Transition of the system with initial conditions from the vicinity of stationary state to an attractor corresponds to the case of a self-excited attractor. However, there exist attractors of another type: hidden attractors are attractors with the basin of attraction which does not have intersection with a small neighborhoods of any equilibrium points. Classification "hidden vs self-excited" attractors was introduced by Leonov and Kuznetsov. Discovery of the hidden chaotic attractor has shown the need for further study of the scenarios concerned with the appearance and properties of hidden attractors, since the appearance of such attractors in the system can lead to a qualitative change in the dynamics of the system. In the present work two directions have been chosen, for which the possibility of the appearance of hidden attractors can be critical: radiophysics and biophysics. The features of radiophysical generators which can be used for systems of secure communication based on the dynamical chaos are considered in detail. Using the Chua circuit as an example, we investigate the problem of synchronization between two coupled generators in case when the observed regimes are represented by hidden and self-excited attractors. This example shows that in case of hidden attractors under certain initial conditions desynchronization of the coupled subsystems is possible, and the system of secure communication becomes inoperative. Alternative new radiophysical generators with self-excited attractors are also proposed. In such generators, the dynamical chaos is stable to the variation of parameters, initial conditions. In the context of the biophysics problems, a simplified model describing the dynamics of beta-cells based on the Hodgkin-Huxley formalism is presented. It has a typical for such systems bursting attractor which became hidden. This model can be used for the description of various pathological states of cells formation.

Bioceramics are biocompatible ceramic materials, that interact with biological systems of the body to treat, strengthen or replace body functions. Most conventional bioceramics are oxide ceramics, glass ceramics and calcium phosphate ceramics. Among these calcium phosphates, synthetic hydroxyapatite has been extensively studied due to its biomimetic properties similar to that of natural bone. One approach to prepare synthetic hydroxyapatite is to first deposit amorphous Ca-P-O thin film and then by means of post deposition annealing initiate the formation of hydroxyapatite crystals to the film. In addition to the correct film composition and crystalline structure, other surface properties such as wettability and surface nano- and microtopography are very significant for the biocompatibility. In this study Ca-P-O thin films were deposited using two different techniques, ion beam sputtering and atomic layer deposition (ALD). Films deposited using both techniques were amorphous after deposition. For sputter deposited films, the Ca/P atomic ratio determined by means of ion beam analysis approached stoichiometric hydroxyapatite when hydroxyapatite powder doped with extra phosphorous was used as the sputtering target. Though the sputtered films showed good biocompatibility in cell attachment studies, the dissolution of as-deposited films in cell culture medium is a disadvantage. The surface of as-deposited and annealed thin films deposited using ALD were locally modified by high and low energy irradiation. After low energy ion irradiation the as-deposited films showed an increase in hydrophilicity, which was determined using contact angle measurements, and also greater spreading of mouse pre-osteoblast cells. The effect of surface topography was studied by abrading Ti metal substrates to different roughnesses before depositing 2–50 nm thick ALD Ca-P-O films on them. Ti was selected in order to combine the biocompatibility of Ca-P-O thin-films with the mechanical strength of the Ti metal substrate. Ca-P-O films deposited on smoother substrates showed higher Ca/P atomic ratios than those on the rough substrates, demonstrating the influence of roughness on the film growth during the deposition. As-deposited Ca-P-O films acted as equally good cell culture substrate as untreated Ti samples used as a control. After post deposition annealing at 800 C, Ca-P-O films were crystallized on Si substrates and showed filopodic morphology of pre-osteoblast cells. Films on Ti showed also filopodic morphology of cells after 700 C annealing but at 800 C the number of cells substantially dropped, most likely due to formation of a less biocompatible TiO2 rutile phase on the surface.

The complexity of life is based on an effective energy transduction machinery, which has evolved during the last 3.5 billion years. In aerobic life, the utilization of the high oxidizing potential of molecular oxygen powers this machinery. Oxygen is safely reduced by a membrane bound enzyme, cytochrome c oxidase (CcO), to produce an electrochemical proton gradient over the mitochondrial or bacterial membrane. This gradient is used for energy-requiring reactions such as synthesis of ATP by F0F1-ATPase and active transport. In this thesis, the molecular mechanism by which CcO couples the oxygen reduction chemistry to proton-pumping has been studied by theoretical computer simulations. By building both classical and quantum mechanical model systems based on the X-ray structure of CcO from Bos taurus, the dynamics and energetics of the system were studied in different intermediate states of the enzyme. As a result of this work, a mechanism was suggested by which CcO can prevent protons from leaking backwards in proton-pumping. The use and activation of two proton conducting channels were also enlightened together with a mechanism by which CcO sorts the chemical protons from pumped protons. The latter problem is referred to as the gating mechanism of CcO, and has remained a challenge in the bioenergetics field for more than three decades. Furthermore, a new method for deriving charge parameters for classical simulations of complex metalloenzymes was developed. Livets mångfald baserar sig på ett effektivt energiproduktionsmaskineri, som utvecklats under de senaste 3,5 miljarder åren. Detta molekylära maskineri, som också kallas för andningskedjan, befinner sig i eukaryotcellens mitokondrier. Andningskedjan drivs av enzymet cytokrom c oxidas (CcO), som förbrukar nästan allt syre som organismen inandas. CcO reducerar syre till vatten och använder mycket effektivt reaktionens frigjorda energi till att flytta vätejoner (protoner) över mitokondriens inre membran. Precis som i ett batteri uppstår det en spänning över mitokondriens membran, vilken används till att utföra energikrävande processer, t.ex. i produktion av cellens energimolekyl ATP. CcO:s allmänna funktionsprincip har varit känd i tre årtionden, och enzymets atomstruktur utreddes för över tio år sedan. Protonpumpningsmekanismen i CcO är ändå tillsvidare okänd. Med denna mekanism menas den molekylära funktionsprincip med vilken den frigjorda energin från syrereduktionen kopplas till protonöverföring över mitokondriens inre membran. Utredning av den exakta pumpmekanismen är av central betydelse inom biokemin och bioenergetiken eftersom CcO utgör grunden för det aeroba livet. Felfunktion i CcO har visats ha samband med många sjukdomar s.s. Parkinsons sjuka och muskeldegenerationssjukdomar. Dessutom reglerar CcO implicit produktionen av syreradikaler, som har samband t.ex. med degradation av muskelvävnad efter hjärtinfarkt och degradation som sker vid föråldring. CcO:s funktion är också av stort intresse för energiproduktionsindustrin eftersom enzymet fungerar likt en bränslecell, fastän mera effektivt. I framtiden kan möjligen CcO:s effektiva funktionsprincip användas som modell i utvecklingen av bioinspirerade bränsleceller. I min avhandling har jag studerat protonpumpningsmekanismen i CcO med hjälp av teoretisk modellering. Beräkningsmodellerna baserar sig på experimentell strukturinformation, samt resultat från många biokemiska och biofysikaliska experiment. Jag har studerat CcO:s dynamik, energetik och struktur i dess katalytiska cykels olika mellansteg. Beräkningsmodellerna som använts baserar sig på både klassisk- och kvantmekanik, vilka löses med hjälp av effektiva superdatorer. Studierna i denna avhandling utmynnade i sex vetenskapliga artiklar. Som resultat av dessa studier identifierades en specifik aminosyra (Glu-242) nära enzymets aktiva centrum, vilken hindrar de pumpade protonerna från att läcka. Denna aminosyra fungerar delvis som en molekylär motors vevaxel. Dessutom föreslogs en mekanism som CcO använder till att aktivera och växla mellan två protonledande kanaler. En ny metod utvecklades också, som kan användas till att modellera komplicerade enzymatiska metallcentra med hjälp av relativt lätta klassiska beräkningar. Denna metod baserar sig på parametrisering av dessa metallcentra med hjälp av tunga kvantkemiska beräkningar. Parametrarna som härleddes för CcO:s metallcentra användes i många arbeten som ingår i denna avhandling. Det viktigaste resultatet är kanske ändå en ny modell på CcO:s protonpumpningsmekanism, som förklarar hur CcO separerar de protoner som används för pumpning, från protonerna som används i syrereduktionen till vatten. Denna princip kallas för "gating" (eng. "gate" – port), och är en av de viktigaste frågorna i utredningen av CcO:s funktionsprincip. Elämän monimuotoisuuden perustana on äärimmäisen tehokas energiantuotantokoneisto, joka on kehittynyt viimeisten 3,5 miljardin vuoden aikana. Tämä hengitysketjuksi kutsuttu molekyylikoneisto sijaitsee eukaryoottisolun mitokondrioissa. Hengitysketjua pyörittää sytokromi-c oksidaasi -entsyymi (CcO), joka käyttää lähes kaiken eliön hengittämästä hapesta. CcO pelkistää hapen vedeksi ja käyttää erittäin tehokkaasti reaktiossa vapautuneen energian siirtääkseen vetyioneita (protoneita) mitokondrion sisäkalvon yli. Aivan kuten sormiparistossa, mitokondrion kalvon yli syntyy jännite, jota hyödynnetään energiaa vaativissa prosesseissa esimerkiksi solun energiamolekyyli ATP:n tuottamisessa. CcO:n yleinen toimintaperiaate on tunnettu jo yli 30 vuoden ajan ja entsyymin atomirakenne selvitettiin yli kymmenen vuotta sitten. CcO:n pumppumekanismi on kuitenkin vielä tuntematon. Pumppumekanismilla tarkoitetaan molekyylitason toimintaperiaatetta, jossa hapen pelkistämisessä vapautunut energia kytketään protonin siirtoon mitokondrion sisäkalvon yli (protonipumppaus). Pumppumekanismin tarkka ymmärtäminen on biokemian ja bioenergetiikan kannalta keskeistä, sillä CcO on hapellisen elämän energiantuotannon perusta. CcO:n toiminnan häiriöiden on osoitettu liittyvän moniin sairauksiin, kuten Parkinsonin tautiin ja lihasrappeumatauteihin. Lisäksi happiradikaalien tuotanto, jota CcO epäsuorasti säätelee, liittyy sydäninfarkteissa syntyviin kudosvaurioihin sekä ikääntymisen aiheuttamaan rappeutumiseen. CcO:n toiminta on myös energiateollisuudelle erittäin kiinnostava kysymys, koska entsyymi toimii polttokennon tavoin, vaikkakin paljon tehokkaammin. Tulevaisuudessa voidaan mahdollisesti käyttää CcO:n tehokasta toimintaperiaatetta mallina bioinspiroitujen polttokennojen kehittämisessä. Väitöskirjassani olen tutkinut CcO:n pumppumekanismia käyttäen teoreettista mallinnusta. Tutkimuksessa käytetyt laskentamallit perustuvat kokeelliseen rakenneinformaatioon sekä useiden biokemiallisten ja biofysikaalisten kokeiden tuloksiin. Olen tutkinut CcO:n dynamikkaa, energetiikkaa ja rakennetta entsyymin katalyyttisen kierron eri välitiloissa käyttäen sekä klassista mekaniikkaa että kvanttimekaniikkaa ja suuren tehon supertietokoneita. Tutkimuksen tulokset on julkaistu kuudessa tieteellisessä julkaisussa. Tutkimuksessa havaittiin, että tietty aminohappo (Glu-242) lähellä entsyymin aktiivista keskusta estää pumpattavia protoneita vuotamasta takaisin. Kyseinen aminohappo toimii siis osittain molekyylitason moottorin kampiakselina. Tutkimuksessa ehdotettiin myös mekanismia, jota CcO käyttää kahden eri protoninjohtokanavan aktivoimiseen ja vuorotteluun. Tutkimuksessa kehitettiin lisäksi uusi menetelmä, jonka avulla voidaan mallintaa entsyymien monimutkaisia metallikeskuksia käyttämällä kevyempiä klassisia laskuja ja raskaista kvanttikemiallista laskuista johdettuja parametreja. Näitä parametreja CcO:n metallikeskuksille käytettiin väitöskirjan muissa töissä. Väitöskirjan tärkeimpänä tuloksena voidaan kuitenkin pitää uutta mallia pumppumekanismista. Mallin avulla voidaan selittää, miten CcO erottelee pumpattavat protonit niistä protoneista, jotka käytetään hapen pelkistämisessä vedeksi. Tätä periaatetta kutsutaan "gating" mekanismiksi (eng. gate – portti, "portitus"), joka on yksi tärkeimpiä kysymyksiä CcO:n toimintaperiaatteen selvittämisessä.

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes. Työssä on käytetty röntgen- ja neutronisäteilyn sirontaa molekyylibiologian kannalta mielenkiintoisten, nanometrin kokoluokkaan kuuluvien rakenteiden tutkimiseen. Tutkitut systeemit ovat proteiineja, proteiinikomplekseja, viruksia ja vihreiden bakteerien fotosynteesin kannalta tärkeä antennikompleksi, klorosomi. Erilaisten rakennetutkimusmenetelmien antamaa informaatiota on yhdistetty sirontamenetelmillä saatavaan matalan resoluution rakennetietoon. Ensimmäisessä osajulkaisussa proteiinin konformaatiomuutosta tutkittiin yhdistämällä ydinmagneettisen resonanssin antama suuntatieto röntgensironnasta määritettyyn konformaatiomuutoksen suuruuteen. Toisessa osajulkaisussa määritettiin proteiiniosasten paikka elektronimikroskopian avulla luodussa virusmallissa neutronisironnan ja kontrastivariaation avulla. Kolmessa viimeisessä osajulkaisussa esitetään uusi malli vihreiden bakteerien fotosynteettisen kompleksin antenniosan rakenteelle ja sen todetaan olevan sopusoinnussa useista eri bakteerilajeista saatujen röntgensironta- ja elektronimikroskopiatulosten kanssa. Karotenoidien vaikutusta rakenteeseen tutkittiin soveltamalla edellä mainittuja menetelmiä bakteereihin, joiden karotenoidisynteesiin vaikuttavat entsyymit oli poistettu geneettisin menetelmin.