352 research outputs found
Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic
No full textPRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent waves of the pandemic, we present a reflection on the use of urgent supercomputing for global societal challenges and crisis management.Peer Reviewed"Article signat per 18 autors/es: Núria López, Luigi Del Debbio, Marc Baaden, Matej Praprotnik, Laura Grigori, Catarina Simões, Serge Bogaerts, Florian Berberich, Thomas Lippert, Janne Ignatius, Philippe Lavocat, Oriol Pineda, Maria Grazia Giuffreda, Sergi Girona, Dieter Kranzlmüller, Michael M. Resch, Gabriella Scipione, and Thomas Schulthess"Postprint (author's final draft
Večskalne simulacije interakcije tekočinskega toka z biološkimi makromolekulami
No full textProteins are natural polymers that play an essential role both in living organisms and in biotechnological applications. While most of the protein\u27s function evolves in the thermodynamic equilibrium, proteins can also be exposed to non-equilibrium states generated by mechanical stress that can impair their structure. As the structure of protein molecules is critically related to their function, any excessive structural change can lead to a reduced activity or a complete loss of it. For this reason, it is necessary to understand and determine the susceptibility of these biomolecules to mechanical stress, and the key to this knowledge is usually hidden in their dynamic response.
In this thesis, we establish a methodology and an analytical framework that allow us to study the effects of acoustic excitations and hydrodynamic shear flow on the internal, rotational, and conformational dynamics of biological macromolecules. To capture the details of this interaction, we need to allow the molecular system to exchange mass and momentum with its surroundings.
This is possible with the open-boundary molecular dynamics (OBMD) method, which enables grand-canonical simulations in and out of equilibrium. In OBMD simulations, the external boundary conditions are imposed on the system by an additional external force without modifying Newton\u27s equations of motion in the bulk. We extend the OBMD method to simulate the propagation of acoustic waves in liquid water described by the mesoscopic dissipative particle dynamics (DPD) and simple point-charge (SPC) water models.
Evaluating density variation for sound waves of different frequencies in the terahertz (THz) range, we show that our particle-based methodology can recover the fluctuating hydrodynamic description of acoustic waves in the continuum limit. Furthermore, we apply the developed methodology to excite low-frequency vibrational motions in the protein. To this end, we show that the sub-THz acoustic excitations enhance the protein\u27s internal dynamics. On the other hand, by subjecting the protein to a shear flow of various strengths, we demonstrate that extraordinarily high shear rates must be applied to observe unfolding, the extent of which depends on the applied shear rate. Furthermore, we show that the protein gains vibrational angular momentum at higher shear rates, which is reflected in higher angular velocity and confirmed by analyzing the contributions to the total kinetic energy of the biomolecule.Proteini so naravni polimeri, ki v živih organizmih opravljajo mnoge za življenje pomembne funkcije. Čeprav svojo funkcijo največkrat opravljajo v termodinamskem ravnovesju, so lahko izpostavljeni tudi mnogim neravnovesnim pogojem, ki nastanejo kot posledica mehanskih napetosti.
Slednje lahko poškodujejo proteinsko strukturo in povzročijo zmanjšanje ali celo popolno izgubo njihove funkcije. Zaradi tega je potrebno razumeti in določiti občutljivost teh biomolekul na mehanske napetosti, pri čemer se ključ do tega znanja običajno skriva v njihovem dinamičnem odzivu.
V doktorskem delu vzpostavimo metodologijo in analitični pristop, ki nam omogočata preučevanje vpliva akustičnih vzbujanj in hidrodinamskega strižnega toka na interno, rotacijsko in konformacijsko dinamiko bioloških makromolekul. Za opis interakcije tekočinskega toka z biomolekulami, pa moramo sistemu omogočiti, da z okolico izmenjuje snov, gibalno količino in energijo. Primerno simulacijsko tehniko predstavlja odprta simulacija molekulske dinamike [ang. open-boundary molecular dynamics (OBMD)], saj omogoča ravnovesne in neravnovesne simulacije sistema v velekanoničnem ansamblu. V simulacijah OBMD zunanje robne pogoje vpeljemo preko dodatne zunanje sile. V doktorskem delu metodo OBMD razširimo tako, da omogoča simulacije širjenja zvočnih valov v tekoči vodi, ki jo opišemo z mezoskopskim modelom disipativne delčne dinamike [ang. dissipative particle dynamics (DPD)].
Z izračunom časovnega poteka gostotnih variacij zvočnih valov v teraherčnem (THz) frekvenčnem območju pokažemo, da je naša metodologija zmožna opisati širjenje zvoka na kontinuumski skali.
Razvito metodologijo uporabimo tudi za vzbujanje nizkofrekvenčnih normalnih načinov nihanja proteina in ugotovimo, da vzbujanje z akustičnimi valovi ustrezne frekvence vzbudi njegovo interno dinamiko. Poleg tega protein izpostavimo še strižnemu toku različnih jakosti in raziščemo njegovo rotacijsko in konformacijsko dinamiko. Prikažemo, da se protein v strižnem toku zvija in razvija, pri čemer je obseg razvitja odvisen od jakosti strižnega toka. Izračunamo tudi, da se sučni del vibracijskega prispevka pri višjih strižnih hitrostih poveča, kar se odraža tudi v večji kotni hitrosti biomolekule in kar potrdimo z analizo prispevkov translacijske, rotacijske in vibracijske energije k skupni kinetični energiji biomolekule
Kontinuumsko modeliranje in simulacija tekočin na nanoskali
No full textNanofluidics, a scientific field exploring nanoconfined fluids, has seen increasing interest in recent years. This interest is in large part due to the fascinating phenomena that occur at such small scales, such as ultra-efficient fluid transport through tubes with diameters of the order of nanometers. The development of computer science and technology in recent years has also allowed for efficient studies of matter at nanoscale. In this thesis, we study fluids at nanoscale with the aid of computer simulations. The thesis is roughly divided into two parts. In the first part, we study fluid flow past and through objects with sizes of the order of nanometers, and in the second part, we study conservation equations for polymer chains and the associated coupling of density and directional fluctuations.
A widely used approach for studying nanoconfined fluids is molecular dynamics. It is, however, computationally expensive, often mandating the use of supercomputers. Hence, in this thesis we resort to the use of a continuum approach. Various recent studies have suggested that Navier-Stokes equations could be valid down to nanometer scale. However, at such small scales, where the ratio between the surface and bulk volume is not small anymore, the physics at the surface becomes increasingly important. The effective no-slip boundary condition, which is the standard boundary condition at macroscale, is no longer valid. At nanoscale, a slip between the fluid and the surface is observed. We thus use the Navier boundary condition, which takes the slip into account by assuming a linear dependence of shear stress at the surface on the relative velocity between the fluid and the solid at the interface. The boundary condition is parametrized by the slip length, which for straight walls represents the depth to which the fluid velocity profile must be extrapolated to vanish.
We perform computational fluid dynamics simulations, subject to the Navier boundary condition, past spherical molecules and through carbon nanotubes. Water flow through carbon nanotubes is subjected to significant slip. This results in energy efficient flow through the carbon nanotubes. Due to this energy efficiency, energy dissipation at the nanotube entrance and exit becomes significant. We thus explore the energy dissipation in the vicinity of carbon nanotube ends. We observe a nonmonotonic dependence of energy dissipation on the slip length. We successfully model and explain the origin of this dependence and accurately predict the optimal slip length at which the energy dissipation is at its minimum.
In light of recent reports of phonon modes of carbon nanotubes and subsequent diffusion enhancements, we explore the influence of the oscillating carbon nanotubes on the water flow. To examine the effect of carbon nanotube oscillations, we employ fluctuating hydrodynamics, in which a random fluctuating stress tensor representing thermal fluctuations is introduced to the Navier-Stokes equations. We solve the equations and derive the diffusion coefficient for the center of mass of water in an oscillating carbon nanotube. We show that in the continuum description, the phonon modes of the carbon nanotubes do not contribute to the diffusion.
In the second part of this thesis, we study the conservation equations for polymer chain melts. In polymer chain melts, the defects in orientational order are closely related to density. This connection is described by the continuity equation, which is polar in its nature. This presents a problem for nematic polymers as the direction cannot be uniquely defined. In case of long polymer chains with abundant chain folding, the polar order disappears while the nematic order is conserved. By performing Monte Carlo simulations, we show that the continuity equation can be applied if we define a “recovered polar order” by introducing chain cuts at chain fold positions. In the last part, we examine the tensorial conservation equation, which is based on the quadrupolar order. In case of polymer chain folding, the quadrupolar order, in contrast to the polar order, is not lost, thus making the tensorial conservation more appropriate compared to the vectorial conservation equation. We perform Monte Carlo simulations of polymer chains in an istoropic phase and show first evidence of presence of the tensorial constraint.Nanofluidika je področje znanosti, ki preučuje dinamiko tekočin na nanoskali. Zanimanje zanjo v zadnjih letih raste zaradi zanimivih fizikalnih pojavov na majhnih skalah, kot je na primer hiter pretok tekočin skozi kanale velikostnega reda nanometra. Razvoj računalniške znanosti in tehnologije v preteklih letih omogoča učinkovito študiranje materije na nanoskali. V tej doktorski disertaciji bomo študirali tekočine na nanoskali z uporabo računalniških simulacij. Disertacija je razdeljena v dva dela. V prvem delu študiramo tok tekočin mimo in skozi objekte z velikostjo reda nanometra. V drugem delu pa študiramo ohranitvene enačbe za polimerne verige in sklopitev fluktuacij gostote in orientacijskega reda.
Široko uporabljen pristop k študiranju tekočin na nanoskali so simulacije molekulske dinamike. Simulacije molekulske dinamike so računsko zahtevne in pogosto zahtevajo uporabo superračunalnikov. Zato v tej doktorski tezi uporabimo kontinuumski pristop. Več raziskav je pokazalo, da so Navier-Stokesove enačbe lahko veljavne vse do nanoskale. Vendar na tako majhnih skalah, ko razmerje med površino in prostornino ni več majhno, postane dogajanje na površini pomembno. Zato standardni robni pogoj brez zdrsa, ki ga uporabimo na makroskali, ni ustrezen. Na nanoskali opazimo zdrs med tekočino in steno na njunem stiku. Za ustrezen opis zdrsa uporabimo Navierov robni pogoj, ki predpostavi linearno odvisnost strižne napetosti na stiku med tekočino in steno od relativne hitrosti med tekočino in steno. Parameter, ki določa Navierov robni pogoj, je zdrsna dolžina. Ta za ravne stene predstavlja globino, do katere moramo ekstrapolirati hitrostni profil tekočine, da bo ta enak nič.
Izvajamo simulacije računske dinamike tekočin mimo sferičnih molekul in skozi ogljikove nanocevke, kjer uporabimo Navierov robni pogoj. Značilnost toka vode skozi ogljikove nanocevke je velik zdrs. Posledica tega velikega zdrsa je energijska učinkovitost toka vode skozi nanocevke. Zaradi energijske učinkovitosti toka vode znotraj ogljikovih nanocevk pridejo do izraza energijske izgube v okolici koncev nanocevk. Študiramo energijske izgube v okolici koncev nanocevk in odvisnost teh energijskih izgub od zdrsne dolžine. Razvijemo model, ki opiše izvor odvisnosti energijskih izgub od zdrsne dolžine n pravilno napove obstoj optimalne zdrsne dolžine, kjer je izguba energije najmanjša.
V luči nedavnih odkritij fononskih načinov v ogljikovih nanocevkah pri toku vode skozi njih in posledičnem povečanju difuzije študiramo vpliv oscilirajočih sten nanocevk na tok tekočin skozi njih. Da bi ustrezno proučili vpliv oscilacij na difuzijo, uporabimo fluktuirajočo hidrodinamiko, kjer v Navier-Stokesove enačbe vključimo termične fluktuacije. Diferencialne enačbe rešimo za primer toka vode skozi dolgo oscilirajočo nanocevko in izpeljemo difuzijsko konstanto vode. Dobljena difuzijska konstanta nam pokaže, da oscilacije sten nanocevk ne vplivajo na difuzijo vode v nanocevki.
V drugem delu teze študiramo ohranitvene zakone polimernih verig. V talinah polimernih verig so defekti orientacijskega reda in gostote tesno povezani. Ta povezava je izražena v kontinuitetni enačbi, ki je vektorske oblike. To predstavlja problem za apolarne verige, ki jim ni mogoče enolično določiti smeri. V primeru dolgih polimernih verig, ki se prepogibajo, to predstavlja problem, ker prisotnost pregibom zmanjša polarni red, medtem ko se nematski red ohranja. Izvajamo simulacije Monte Carlo talin polimernih verig v nematični fazi. S simulacijami pokažemo, da z uvedbo »popravljenega polarnega reda« kontinuitetna enačba velja tudi v prisotnosti pregibov polimernih verig. Na koncu raziščemo tenzorski ohranitveni zakon, ki je osnovan na kvadrupolnem redu. V primeru pregibanj polimernih verig se kvadrupolni red, za razliko od polarnega, ohranja in je zato tenzorski ohranitveni zakon za apolarne verige primernejši od vektorskega. Izvajamo simulacije Monte Carlo talin polimernih verig v izotropni fazi. V simulacijah odkrijemo prve indikacije fenomenov, ki so posledica tenzorskega ohranitvenega zakona
Odhad momentů při intervalovém cenzorování typu I
No full textTitle: Moments Estimation under Type I Interval Censoring Author: Matej Ďurčík Department: Faculty of Probability and Mathematical Statistics Supervisor: RNDr. Arnošt Komárek Ph.D. Abstract: In this thesis we apply the uniform deconvolution model to the interval censoring problem. We restrict ourselves only on interval censoring case 1. We show how to apply uniform deconvolution model in estimating the probability distribution characteristics in the interval censoring case 1. Moreover we derive limit distributions of the estimators of mean and variance. Then we compare these estimators to the asymptotically efficient estimators based on the nonparametric maximum likelihood estimation by simulation studies under some certain distributions of the random variables.
DEVELOPMENT OF CONTENT ON DEMAND SYSTEM ON XBMC PLATFORM
No full textV diplomski nalogi predstavljamo razvoj sistema vsebin na zahtevo na XBMC platformi. V nalogi predstavimo infrastrukturo sistema IPTV, pripadajoče storitve ter module sistema. Za sistem UMB-SmartTV smo razvili tudi nov XBMC vtičnik za pregled lastnih vsebin. Vtičnik omogoča pregled in predvajanje različnih vsebin na sistemu UMB SmartTV, ki jih lahko uporabnik dodaja v bazo sistema. Podatke o vsebinah je mogoče pregledovati glede na želene kategorije: žanr, leto nastanka, režiser, igralci, avtor itd. Poudarek pri razvoju sistema smo namenili čim hitrejšemu iskanju vsebin, kar smo dosegli tudi z razvrščanjem vsebin v kategorije.The purpose of the diploma thesis is to introduce the development of a Content-on-Demand system on the XBMC platform. The thesis deals with the architecture of the IPTV system, the services that are delivered through this system and its modules. Furthermore we have developed a new XBMC plugin for the content review for the UMB-SmartTV system. The plugin allows the user to view and play various contents that can be added to the system’s database on the UMB-SmartTV system. The user is able to review the information about the content by selecting between different categories like genre, director, actors, author etc. The main goal was to develop a system that provides fast search for specific content and the classification of the content into categories that can help us to access it
Vícečetné zarovnávání sekvencí
No full textNázev práce: Vícečetné zarovnávání sekvencí Autor: Matej Ferenc Katedra (ústav): Katedra aplikované matematiky Vedoucí bakalářské práce: RNDr. Ondřej Pangrác, Ph.D. e-mail vedoucího: [email protected] Abstrakt: V práci študujeme problém zarovnania viacerých proteínových alebo DNA sekvencií. Existuje mnoho prístupov k jeho riešeniu, pričom niektoré algoritmy sú optimalizované na rýchlosť, iné na kvalitu zarovnania. Implementujeme dve metódy - iteratívnu a progresívnu, ktoré vychádzajú z rovnakého princípu: použiť vývojové stromy, pomocou ktorých zostavíme zarovnanie. Zavedieme niekoľko metód na výpočet vzdialenosti sekvencií. Cieľom práce je porovnať jednotlivé metódy pre zarovnanie a zistiť, kedy je ich vhodné použiť a tiež nájsť parametre, pomocou ktorých dosiahneme najlepšie výsledky zarovnania. Klíčová slova: bioinformatika, zarovnanie, sekvencieTitle: Multiple Sequence Alignment Author: Matej Ferenc Department: Department of Applied Mathematics Supervisor: RNDr. Ondřej Pangrác, Ph.D. Supervisor's e-mail address: [email protected] Abstract: In this work we study multiple sequence alignment problem, for aligning protein or DNA sequences. There is a lot of ways how to solve this problem. Some of them are optimized for speed, while others are optimized for quality of the produced alignment. We implement two methods - progressive and iterative, which are based on creating a phylogeny tree and align sequences according to it. We will also provide a few distance methods. Our aim is to compare the methods and their parameters for creating best alignments and to find out, when to use which methods. Keywords: bioinformatics, alignment, sequencesDepartment of Applied MathematicsKatedra aplikované matematikyFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult
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