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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
Get PDFNanofluidics, 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
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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