Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.

Contractive metrics for a Boltzmann equation for granular gases: diffusive equilibriaThe Patterson-Sullivan embedding and minimal volume entropy for outer space

We quantify the long-time behavior of a system of (partially) inelastic particles in a stochastic thermostat by means of the contractivity of a suitable metric in the set of probability measures. Existence, uniqueness, boundedness of moments and regularity of a steady state are derived from this basic property. The solutions of the kinetic model are proved to converge exponentially as t→ ∞ to this diffusive equilibrium in this distance metrizing the weak convergence of measures. Then, we prove a uniform bound in time on Sobolev norms of the solution, provided the initial data has a finite norm in the corresponding Sobolev space. These results are then combined, using interpolation inequalities, to obtain exponential convergence to the diffusive equilibrium in the strong L¹-norm, as well as various Sobolev norms.

Driven fragmentation of granular gases

The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the longvelocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f (c)~exp (−cⁿ), with n ≈1.2, regarding less the fragmentation mechanisms

Haihdutusnopeuksien määritys glysiinin alipainekiteytyksessä

Alipainekiteytyksessä tasalaatuisen lopputuotteen valmistamiseksi kiteytysolosuhteiden vaikutus liuottimen haihtumisvuohon ja kiteiden ominaisuuksiin on huomioitava. Kandidaatin työn tavoitteena oli selvittää, miten glysiinin alipainekiteytyksessä vesiliuoksesta kiteytysolosuhteet (lämpötila ja paine) vaikuttavat liuottimen haihtumisvuohon ja syntyvien kiteiden polymorfiaan. Haihdutuskokeet suoritettiin puhtaalle vedelle ja alipainekiteytyskokeet glysiinin 95 % kylläiselle vesiliuokselle lämpötiloissa 40 °C, 50 °C ja 60 °C ja paineissa 40 mbar, 60 mbar ja 80 mbar. Kiteyttimenä käytettiin suljettua, virtaushaitoilla, sekoittimella ja ohjausputkella varustettua reaktoria johon oli kytketty alipainepumppu ja termostaatti paineen ja lämpötilan ohjaamiseksi. Nesteen määrä haihdutuskokeissa oli 2 kg ja alipainekiteytyskokeissa 1,2 kg. Osa alipainekiteytyskokeista saaduista kiteistä analysoitiin jauheröntgendiffraktioanalysaattorin (PXRD, engl. powder x-ray diffraction) avulla. Kaikki PXRD-laitteella analysoidut alipainekiteytyskokeissa saadut kiteet osoittautuivat glysiinin γ-polymorfiksi. Kiteytysolosuhteilla oli selkeä vaikutus haihtumisvuohon, mutta vaikutusta glysiinikiteiden polymorfiaan ei havaittu koealueella.

Lämminvesivaraajan ohjaus automaatiolla aurinkosähköä tuottavassa kotitaloudessa

Hajautettu sähköntuotanto aurinkopaneeleilla on Suomessa kasvussa. Kotitalouksiin asennettujen aurinkopaneelijärjestelmien määrä kasvaa jatkuvasti, mutta suuri osa tuotetusta sähköenergiasta syötetään sähköverkkoon. Tämä johtuu aurinkosähkön tuotannon painottumisesta kesäpäiviin, jolloin kotitalouksien kulutus on pienimmillään. Suurin hyöty itse tuotetusta energiasta saadaan kuitenkin käyttämällä se tuotantokohteessa, jolla minimoidaan energiansiirto sähköverkon ja kotitalouden rajapinnassa. Siirtämällä kotitalouden suurimpia kuormia aurinkosähkön mukaan ohjatuksi, voidaan saavuttaa merkittäviä parannuksia tuotetun sähkön omakäyttöasteessa. Helpoimmillaan tämä onnistuu kellokytkimellä, joka ajoittaa kulutuksen parhaimman tuotannon ajalle. Tämä ei kuitenkaan poista ongelmaa tilanteissa, jossa aurinkosähkön tuotanto on häiriintynyt esimerkiksi pilvisyyden takia aamupäivällä ja huipputuotanto saavutetaan vasta iltapäivän puolella. Saatavilla on jo useita järjestelmiä, jotka ohjaavat kodin laitteita tuotannon mukaisesti. Suuri osa näistä järjestelmistä on kuitenkin suunniteltu toimimaan vain tuotetun energiamäärän mukaisesti, ottamatta huomioon kotitaloudessa olevaa muuta, automaation piiriin kuulumatonta kulutusta. Tässä kandidaatin työssä vertaillaan sähköenergian eri mittaustapoja ja niiden vaikutusta siirretyn energian laskennalliseen määrään. Lisäksi työssä tutkitaan lämminvesivaraajan kuormanohjausta käyttäen termostaatti-, kellokytkin- ja logiikkaohjausta. Työssä esitelty logiikkaohjaus hyödyntää siirretyn energian mittausta sähköverkon ja kotitalouden rajapinnassa, ottaen automaattisesti huomioon myös talouden muun kulutuksen. Työssä esitellään myös esimerkkilaitteisto, jolla suunniteltu logiikka voidaan toteuttaa.

Natural freeze crystallization : purification of aqueous Na2SO4 solutions with cold air

The aim of this thesis was to examine efficiency of freeze crystallization and eutectic freeze crystallization in purification of wastewater by imitating natural freezing. In addition, a mathematic model based on heat transfer to determine ice thickness and ice growth rate was examined. Also, the amount of sodium sulfate crystallized at the eutectic point was under investigation. In literature part, advantages and applications of the freeze crystallization are discussed, and possibility to apply it in Northern hemisphere winter weather conditions is under study. Furthermore, main sources of sodium sulfate from Finnish industries are described. The experiments were carried out in modified chest freezer, where a fan was placed in order to obtain laminar air flow inside. Picolog PT-104 data logger was used to monitor temperature changes in the salt-water solution, and constant temperature was maintained in the crystallizer with Lauda RP 850 thermostat. The impurity of formed ice layer was determined by weighing ice samples after experiment and again after 24 hours drying to full dryness in oven. Volume of salt-water solution was also measured after experiment. The highest purity of formed ice layer was obtained with small temperature difference and with long freezing time. On the other hand, the amount of crystallized sodium sulfate was its greatest with long freezing time and higher temperature difference. The results obtained by the mathematic model and empirical results did not differ significantly in most of the experiments. However, the difference increased when salt-water mixture reached its eutectic point, leading to simultaneous ice and salt crystallization. Eutectic point was reached only with the highest salt concentration with one exception. In these cases, calculated values were in many cases greater than the experimental ones. In winter weather conditions freeze crystallization is cost-effective wastewater treatment method and rather simple. Nonetheless, the efficiency and separation rate are strongly depended on ambient temperature and its changes

Molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferrosolids the observed susceptibility is considerably lowered when compared to ferrofluids.

Passive solar options for reducing heating demand and maintain indoor climate in a multifamily house in Sweden

This research was carried out by studying possible renovation of a two-storey detached multifamily building by using passive solar design options in a cold climate in Borlänge, Sweden where the heating Degree Days are 4451 (base 20°C). Borlänge`s housing company, Tunabyggen, plans to renovate the project house located inthe multicultural district, Jakobsgårdarna. The goal of the thesis was to suggest a redesign of the current building, decrease the heating energy use, by applying passive solar design and control strategies, in a most reasonable way. In addition ensure a better thermal comfort for the tenants in the dwellings. Literatures have been studied, from which can be inferred that passive design should be abasic design consideration for all housing constructions, because it has advantages to ensure thermal comfort, and reduce the energy use. In addition further savings can be achieved applying different types of control strategies, from which the house will be more personalized, and better adapted to the user’s needs.The proposed method is based on simulations by using TRNSYS software. First a proper building model was set up, which represents the current state of the project building. Then the thermal insulation and the windows were upgraded, based on today's building regulations. The developments of the passive solar options were accomplished in two steps. First of all the relevant basic passive design elements were considered, then those advantages were compared to the advantages of applying new conventional thermostat, and shading control strategies.The results show that there is significant potential with the different types of passive solar design; their usage depends primarily on the location of the site as well as the orientation of the project building. Applying the control strategies, such as thermostat, and shading control, along the thermal insulation upgrade, may lead to significant energy savings (around 40 %), by comparison to the reference building without any upgrade.

Colina em rações para tilápia do Nilo: desempenho produtivo e respostas hematológicas antes e após o estímulo a frio

Pós-graduação em Zootecnia - FMVZ

Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.

Predicting the Mechanical Properties of Carbon-Based Materials Using Molecular Dynamics

The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although molecular modeling has been used extensively to predict elastic properties of materials, modeling of more complex phenomenon such as fracture has only recently been possible with the development of new force fields such as ReaxFF, which is used in this work. It is not fully understood what molecular modeling parameters such as thermostat type, thermostat coupling, time step, system size, and strain rate are required for accurate modeling of fracture. Selection of modeling parameters to model fracture can be difficult and non-intuitive compared to modeling elastic properties using traditional force fields, and the errors generated by incorrect parameters may be non-obvious. These molecular modeling parameters are systematically investigated and their effects on the fracture of well-known carbon materials are analyzed. It is determined that for coupling coefficients of 250 fs and greater do not result in substantial differences in the stress-strain response of the materials using any thermostat type. A time step of 0.5 fs of smaller is required for accurate results. Strain rates greater than 2.2 ns-1 are sufficient to obtain repeatable results with slower strain rates for the materials studied. The results of this study indicate that further refinement of the Chenoweth parameter set is required to accurately predict the mechanical response of carbon-based systems. The ReaxFF has been used extensively to model systems in which bond breaking and formation occur. In particular ReaxFF has been used to model reactions of small molecules. Some elastic and fracture properties have been successfully modeled using ReaxFF in materials such as silicon and some metals. However, it is not clear if current parameterizations for ReaxFF are able to accurately reproduce the elastic and fracture properties of carbon materials. The stress-strain response of a new ReaxFF parameterization is compared to the previous parameterization and density functional theory results for well-known carbon materials. The new ReaxFF parameterization makes xv substantial improvements to the predicted mechanical response of carbon materials, and is found to be suitable for modeling the mechanical response of carbon materials. Finally, a new material composed of carbon nanotubes within an amorphous carbon (AC) matrix is modeled using the ReaxFF. Various parameters that may be experimentally controlled are investigated such as nanotube bundling, comparing multi-walled nanotube with single-walled nanotubes, and degree of functionalization of the nanotubes. Elastic and fracture properties are investigated for the composite systems and compared to results of pure-nanotube and pure-AC models. It is found that the arrangement of the nanotubes and degree of crosslinking may substantially affect the properties of the systems, particularly in the transverse directions.

Plio-Pleistocene Mg/Ca and TEX86 sea surface temperature records of ODP Sites 184-1143 and 165-999,

The western warm pools of the Atlantic and Pacific oceans are a critical source of heat and moisture for the tropical climate system. Over the past five million years, global mean temperatures have cooled by 3-4 °C. Yet, current reconstructions of sea surface temperatures indicate that temperature in the warm pools has remained stable during this time. This stability has been used to suggest that tropical sea-surface temperatures are controlled by some sort of thermostat-like regulation. Here we reconstruct sea surface temperatures in the South China Sea, Caribbean Sea and western equatorial Pacific Ocean for the past five million years, using a combination of the Mg/Ca, TEXH86-and Uk'37 surface temperature proxies. Our data indicate that during the period of Pliocene warmth from about 5 to 2.6 million years ago, the western Pacific and western Atlantic warm pools were about 2 °C warmer than today. We suggest that the apparent lack of warming seen in the previous reconstructions was an artefact of low seawater Mg/Ca ratios in the Pliocene oceans. Taking this bias into account, our data indicate that tropical sea surface temperatures did change in conjunction with global mean temperatures. We therefore conclude that the temperature of the warm pools of the equatorial oceans during the Pliocene was not limited by a thermostat-like mechanism.

Strontium and oxygen isotope data for DSDP Hole 44-390A and ODP Leg 171 holes

Differences in regional responses to climate fluctuations are well documented on short time scales (e.g., El Niño-Southern Oscillation), but with the exception of latitudinal temperature gradients, regional patterns are seldom considered in discussions of ancient greenhouse climates. Contrary to the expectation of global warming or global cooling implicit in most treatments of climate evolution over millions of years, this paper shows that the North Atlantic warmed by as much as 6°C (1.5% decrease in d18O values of planktic foraminifera) during the Maastrichtian global cooling interval. We suggest that warming was the result of the importation of heat from the South Atlantic. Decreasing North Atlantic d18O values are also associated with increasing gradients in planktic d13C values, suggesting increasing surface-water stratification and a correlated strengthening of the North Atlantic Polar Front. If correct, this conclusion predicts arctic cooling during the late Maastrichtian. Beyond implications for the Maastrichtian, these data demonstrate that climate does not behave as if there is a simple global thermostat, even on geologic time scales.

Sistema de control de temperatura a través de Arduino y la tecnología GPRS/GSM

El principal objetivo de este proyecto consiste en estudiar las posibilidades de desarrollo de un sistema para el control de la temperatura basado en la plataforma Arduino. Con el fin de alcanzar dicho objetivo, se ha implementado un sistema que permite la consulta y control de la temperatura ambiente a través de la red de comunicaciones móviles. Tras un análisis previo de las distintas placas Arduino, se evalúan una serie de módulos de expansión (shields) compatibles con dicha plataforma que nos permiten ampliar sus funcionalidades, dotando al dispositivo de un sistema de comunicación basado en la tecnología GPRS/GSM. Se estudian los diferentes sensores de temperatura compatibles con Arduino, además de una serie de actuadores que contribuyen al accionamiento y control de un posible termostato, así como al desarrollo de un pequeño sistema de alarma capaz de detectar temperaturas extremas. El proyecto concluye con el diseño de una aplicación basada en el entorno de desarrollo Arduino que nos permita evaluar las distintas capacidades de nuestro sistema, así como comunicarnos con la plataforma a través de SMS para el control remoto de la temperatura. ABSTRACT. The goal of the project consists of studying the developmental possibilities of a temperature control system based on the Arduino platform. In order to this, there has been implemented a system to consult and manage the environmental temperature through mobile communication networks. After a previous assessment of the different Arduino boards, there are analysed a set of expansion modules (shields) compatibles with the platform that enables us to upgrade the device functionalities with the GPRS/GSM communication protocol. Different temperature sensors compatible with Arduino have been studied. In addition, there are evaluated a set of actuators for the operation and control of a thermostat and also the development of a small alarm system that alerts of extremes temperatures. The project concludes with the design of an application based on the Arduino development environment which allows us to evaluate the different capabilities of our system as well as the communication with the platform by SMS for the remote temperature control.

Effects of internal gain assumptions in building energy calculations /

The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. This paper describes the effects of typical internal gain assumptions in energy calculations. The results of this study indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variation in internal gains.