Native structure-based modeling and simulation of biomolecular systems per mouse click

Background Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. Results Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. Conclusions We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research

Supplying Europe with Hydrogen and Negative Emissions – A Model-Based Assessment

Elektrolysewasserstoff und aus der Umgebungsluft abgeschiedenes und anschließend eingespeichertes CO2 (DACCS) sind zwei Optionen für die Umsetzung ambitionierter Klimaschutzstrategien in Deutschland und Europa. Strombasierter Wasserstoff kann dabei potentiell fossile Energieträger in vielen Prozessen und Anwendungen der klassischen Energienachfragesektoren ersetzen und im Umwandlungssektor als saisonaler Energiespeicher fungieren. Negative Emissionen mittels DACCS können unvermeidbare Restemissionen, z. B. aus der Landwirtschaft, kompensieren und in ökonomische Konkurrenz mit alternativen Treibhausgasminderungsstrategien treten. Beide Optionen interagieren stark mit einem im Wandel befindlichen Energieangebotssystem. Ziel dieser Dissertation ist deshalb die quantitative Analyse der Wechselwirkungen des Wasserstoffsystems mit dem Umwandlungssektor und der Bereitstellung von Negativemissionen mittels DACCS im Kontext eines treibhausgasneutralen europäischen Energiesystems. Zur Adressierung des Forschungsgegenstandes wird das auf die Abbildung von Strom- und Wärmebereitstellung ausgerichtete Kostenminimierungsmodell Enertile zu einem multidirektionalen Energieangebotsmodell erweitert. Kern der methodischen Weiterentwicklung ist die Modellierung der Interaktionen von Wasserstoff- und DACCS-Technologien mit zukünftig auf erneuerbare Energien ausgelegten Strom- und Wärmesystemen. An Hand von Szenariostudien werden Potentiale von Wasserstoff und DACCS bestimmt und wesentliche Treiber für ihre Nutzung identifiziert. Für Wasserstoff zeigen die Modellergebnisse, dass Europa ein substantielles Wasserstofferzeugungspotential hat und sich in großen Teilen kosteneffizient selbstversorgen kann. Elektrolyseure und Wasserstoffkraftwerke werden zu zentralen Flexibilitätsgebern im optimierten erneuerbaren Stromsystem. Die Wasserstofferzeugung folgt dabei der kostengünstigen erneuerbaren Stromerzeugung. In der Kostenminimierung übernehmen Wasserstoffspeicher mit einem saisonalen und Wasserstofftransportnetze mit einem überregionalen Ausgleich von Angebot und Nachfrage fundamentale Aufgaben im Energiesystem. In den Modellergebnissen für Europa gibt es DACCS-Potentiale zu Kosten zwischen 60 und 270 €/tCO2. Im Literaturvergleich können diese technischen Negativemissionen mit vergleichsweise teuren, alternativen Treibhaugasminderungsoptionen konkurrieren. In der Optimierung erfüllen Schweden, die Iberische Halbinsel, Norwegen, und Finnland zentrale Voraussetzungen für geeignete DACCS-Standorte: Ungenutzte Stromerzeugungs- und geologische Speicherpotentiale. Diese Dissertation wurde im Rahmen meiner Forschungsarbeit am Fraunhofer-Institut für System- und Innovationsforschung (ISI) erstellt und von Prof. Dr. Martin Wietschel am Institut für industrielle Produktion (IIP) des Karlsruher Instituts für Technologie (KIT) betreut. Dr. rer. pol. ist der angestrebte Abschluss

Elektrokeemilise voogkondensaatori arendamine ja optimiseerimine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneElektrokeemiline voogkondensaator (EFC) on kontseptuaalne lahendus elektrienergia mastaapseks salvestamiseks. Kõnealune seade sarnaneb tööpõhimõttelt superkondensaatorile, aga olulise erinevusena kasutab tahkete elektroodide asemel süsniniku mikro ja nano-osakestest ning elektrolüüdist koosnevat suspensiooni. Elektrolüüdiga suspensioon on eraldatud poorse, ioonjuhtiva membraaniga ja seadmes on tüüpiliselt mõne millimeetrilise diameetriga kanalid, mille sein on voolkollektoriks ning millest pumbatakse läbi eelpool kirjeldatud suspensiooni. Just nimelt süsinikupõhiste vedelate elektroodide kasutamine võimaldab arendatavat seadet olulisel määral skaleerida ning tulevikus integreerida olemasolevatesse elektrivõrkudesse ja/või rakendada seda efektiivselt taastuvate energiaallikate poolt toodetud elektrienergia salvestamiseks. Doktoritöö keskseks eesmärgiks on EFC-tehnoloogia fundamentaalsete omaduste interpreteerimine. Sellest tulenevalt on töös on läbi viidud EFC elektrokeemilised karakteriseerimised ja arvutisimulatsioonid seadme disainlahenduste optimeerimiseks. Simulatsioonide valdkonnas on sobitatud EFC modelleerimiseks nii olemasolevaid elektrokeemilisi mudeled kui on arendatud ka uudne nn stohhastiline Monte-Carlo põhimõtetel baseeruv mudel. Väljatöötatud mudelid kalibreeriti ja valideeriti põhjalikult võrdluses elektrokeemiliste tulemustega ning neid kasutati voogelektroodide laadimisprotsessi sügavamaks mõistmiseks kolmes fundamentaalses EFC-seadme konstruktsioonis. Sarnaste elektrokeemiliste seadmete modelleerimiseks kasutatakse tihti Nernst-Planki võrranditel või kontsentreeritud lahuse teooriatel baseeruvaid mudeleid. Luuakse teist järku osatuletsitega diferentsiaalvõrrandite süsteemid, mis kirjeldavad nii ioonide kontsentratsioone kui ka seadmes tekkivaid laenguülekande protsesse. Nende mudelite rakendamine iseloomustas ilmekalt difusiooni tõttu seadmes tekkivaid laengu salvestamise ja osakeste transpordi piiranguid. Efektiivne elektroodimaterjali tsirkulatsioon ning piisavalt kiire laengu transport on teineteisele vastanduvad protsessid – kui esimesel juhul on oluliseks näitajaks piisavalt suur elektroodi voolukanalite diameeter, siis teisel juhul on nõutav just nimelt sama kanali diameetri minimiseerimine. Samas ilmnes eksperimentaalsest tulemustest, et mitte ainult difusioonist tingitud nähtused pole olulised, vaid märkimisväärset mõju omavad ka nn kõrvalreaktsioonid. Töö käigus loodud stohhastiline mudel võimaldas saavutada edukalt elektrokeemiliste mõõtmistulemuste ning Nernst-Planki võrranditel baseeruvate mudelitega leitud tulemuste kokkulangevuse. Enamgi, loodud stohhastiline mudel võimaldab edukalt simuleerida vedelate elektroodide laadumise dünaamikat ja kirjeldada suspensioonis asetleidvaid protsesse ning hinnata kõrvalreaktsioonide mõjusid. Kokkuvõtvalt avab loodud lähenemisviis võimaluse leidmaks lahendust voogkondensaatori disaini kesksele probleemile – kuidas tagada seadmest piisav elektroodimaterjali läbivool ning samas hoiduda laengu transpordi limiteerimisest difusiooni tõttu. EFC-tehnoloogia edasise arengu puhul võib eeldada taastuvatest allikatest toodetud energia salvestamisvõimsuse märkimisväärset kasvu. Samas tuleb lisada, et EFC võimsustiheduse parandamiseks, ilma et see kahjustaks nende seadmete energiatihedust ning tsükleeritavust, on vaja jälgida arenduste kooskõla ka muude energiasalvestus- ja muundamis-tehnoloogiatega. Olulisteks faktoriteks on nii seadme töötingimuste valik, elektroodide disain, elektrolüüdi materjalid, kuid samuti ka sobilikud katalüsaatorid.An electrochemical flow capacitor (EFC) is a conceptual approach to meet large-scale electricity storage. This device is similar in operation to a supercapacitor but uses a concentrated solution of carbon micro and nanoparticles and an electrolyte instead of solid electrodes. It typically flows in channels with a diameter of a few millimeters, the wall of which is a flow collector and through which the liquid electrode material is pumped. A porous ion-conducting membrane separates the electrodes. Using carbon-based liquid electrodes in the device under development will allow the technology to be significantly scaled up and integrated into existing electricity grids and used effectively to support renewable energy production. The central goal of the work presented is to understand the fundamental properties of EFC technology. As a result, EFC laboratory tests and computer simulations have been performed to design and optimize the device architecture. In the field of simulations, both existing electrochemical models have been adapted for EFC modeling, and a new stochastic model based on Monte-Carlo principles has been developed. Both implemented and developed models were thoroughly calibrated and validated against laboratory experiments and used to understand the flow electrode charging process in three fundamental EFC device designs. Models based on Nernst-Planck equations or concentrated solution theories are often used to model similar electrochemical devices. Second-order differential equations systems with partial derivatives describe both the ion concentrations and the charge exchange processes occurring in the device. The application of these models was characterized by the limitations of charge storage and transport processes in the device due to diffusion. If the electrode material circulation and sufficiently fast charge transport are critical processes, then a sufficiently large diameter of the electrode flow channels is important. Otherwise, it is necessary to minimize the diameter of the same channel. At the same time, the experimental work showed that the phenomena caused by diffusion are critical side effects and have a significant effect on electrode charging processes. The models based on the Nernst-Planck equations and the stochastic model developed successfully matched the experimental results. Moreover, the developed stochastic model allows to simulate the convection and mixing processes of liquid electrodes successfully and to apply the effects of side reactions. Thus, the developed approach opens the possibility to find a solution to the central problem of the flow capacitor design - how to ensure sufficient flow of electrode material from the device and at the same time avoid limiting the transport of charge due to diffusion. Due to the development of EFC technology, a significant increase in the storage capacity of energy from renewable sources can be expected. At the same time, to improve the power density of EFCs without compromising their high energy density and cyclicality, it is necessary to monitor the coherence of developments with other energy storage and conversion technologies. Important factors are the choice of operating conditions of the device, the design of the electrodes, the materials of the electrolyte, as well as suitable catalysts.https://www.ester.ee/record=b549496

Science-based solutions to foster connectivity of wolf populations are limited by available data

European wolf populations are currently exposed to distinct sources of anthropogenic disturbance and mortality that can cause dispersal limitations and lead to isolation. The identification of factors that act as complete or partial barriers to movement, dispersal, or gene flow contribute to foster connectivity between populations. We reviewed the existing literature (N=32) on wolf population barriers to 1) identify main barriers to connectivity; 2) outline different methodologies; and 3) highlight knowledge gaps. Based on the reviewed studies that empirically tested barrier occurrence (N=14), we compiled data on wolf population structure, anthropogenic disturbance, land cover, ecological factors, geographical features, and prey availability, and tested them as predictors to explain barrier occurrence at continental scale. We report few studies directly addressing this subject for one of the most emblematic and thoroughly studied species, inhabiting one of the most modified landscapes in the world. Albeit our analysis suggested that anthropogenic features are the main drivers of barrier occurrence, we highlight that the absence of standardised data limits our understanding of this subject. Long-term, intensive monitoring programs, explicit hypothesis-driven research using empirical methodologies, and the integration of information on databases for collaborative science are needed to increase the conservation and management relevance of future scientific outcomes on this topic.info:eu-repo/semantics/publishedVersio

Metallic water: transient state under ultrafast electronic excitation

The modern means of controlled irradiation by femtosecond lasers or swift heavy ion beams can transiently produce such energy densities in samples that reach collective electronic excitation levels of the warm dense matter state where the potential energy of interaction of the particles is comparable to their kinetic energies (temperatures of a few eV). Such massive electronic excitation severely alters the interatomic potentials, producing unusual nonequilibrium states of matter and different chemistry. We employ density functional theory and tight binding molecular dynamics formalisms to study the response of bulk water to ultrafast excitation of its electrons. After a certain threshold electronic temperature, the water becomes electronically conducting via the collapse of its band gap. At high doses, it is accompanied by nonthermal acceleration of ions to a temperature of a few thousand Kelvins within sub-100 fs timescales. We identify the interplay of this nonthermal mechanism with the electron-ion coupling, enhancing the electron-to-ions energy transfer. Various chemically active fragments are formed from the disintegrating water molecules, depending on the deposited dose.Comment: to be submitte

Systems Biology in ELIXIR: modelling in the spotlight

info:eu-repo/semantics/publishedVersio

Systems Biology in ELIXIR: modelling in the spotlight

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR\u27s future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives

Reducing Training Data Needs with Minimal Multilevel Machine Learning (M3L)

For many machine learning applications in science, data acquisition, not training, is the bottleneck even when avoiding experiments and relying on computation and simulation. Correspondingly, and in order to reduce cost and carbon footprint, training data efficiency is key. We introduce minimal multilevel machine learning (M3L) which optimizes training data set sizes using a loss function at multiple levels of reference data in order to minimize a combination of prediction error with overall training data acquisition costs (as measured by computational wall-times). Numerical evidence has been obtained for calculated atomization energies and electron affinities of thousands of organic molecules at various levels of theory including HF, MP2, DLPNO-CCSD(T), DFHFCABS, PNOMP2F12, and PNOCCSD(T)F12, and treating tens with basis sets TZ, cc-pVTZ, and AVTZ-F12. Our M3L benchmarks for reaching chemical accuracy in distinct chemical compound sub-spaces indicate substantial computational cost reductions by factors of $\sim$ 1.01, 1.1, 3.8, 13.8 and 25.8 when compared to heuristic sub-optimal multilevel machine learning (M2L) for the data sets QM7b, QM9$^\mathrm{LCCSD(T)}$, EGP, QM9$^\mathrm{CCSD(T)}_\mathrm{AE}$, and QM9$^\mathrm{CCSD(T)}_\mathrm{EA}$, respectively. Furthermore, we use M2L to investigate the performance for 76 density functionals when used within multilevel learning and building on the following levels drawn from the hierarchy of Jacobs Ladder:~LDA, GGA, mGGA, and hybrid functionals. Within M2L and the molecules considered, mGGAs do not provide any noticeable advantage over GGAs. Among the functionals considered and in combination with LDA, the three on average top performing GGA and Hybrid levels for atomization energies on QM9 using M3L correspond respectively to PW91, KT2, B97D, and $\tau$-HCTH, B3LYP$\ast$(VWN5), TPSSH

Perspectives of Nuclear Physics in Europe: NuPECC Long Range Plan 2010

The goal of this European Science Foundation Forward Look into the future of Nuclear Physics is to bring together the entire Nuclear Physics community in Europe to formulate a coherent plan of the best way to develop the field in the coming decade and beyond.<p></p> The primary aim of Nuclear Physics is to understand the origin, evolution, structure and phases of strongly interacting matter, which constitutes nearly 100% of the visible matter in the universe. This is an immensely important and challenging task that requires the concerted effort of scientists working in both theory and experiment, funding agencies, politicians and the public.<p></p> Nuclear Physics projects are often “big science”, which implies large investments and long lead times. They need careful forward planning and strong support from policy makers. This Forward Look provides an excellent tool to achieve this. It represents the outcome of detailed scrutiny by Europe’s leading experts and will help focus the views of the scientific community on the most promising directions in the field and create the basis for funding agencies to provide adequate support.<p></p> The current NuPECC Long Range Plan 2010 “Perspectives of Nuclear Physics in Europe” resulted from consultation with close to 6 000 scientists and engineers over a period of approximately one year. Its detailed recommendations are presented on the following pages. For the interested public, a short summary brochure has been produced to accompany the Forward Look.<p></p&gt