Molecular Dynamics Studies of Nanofluidic Devices

Abstract

Nanoteknologi og fluid mekanik er to videnskabelige områder, hvor de senestefremskridt har afsløret en række nye teknologiske og videnskabelige muligheder.Fremskridtene i begge felter giver mulighed for tværfaglige metoder og de seneste resultater lover mulighed for nye anvendelser, der kan føre til en teknologisk revolution. Nye nanofabrikationsteknikker har åbnet muligheder for udvikling af små integrerede enheder, så som lab-on-a-chip for biokemisk syntese og analyse. Integration opnås ved miniaturisering af funktionelle elementer f.eks. af kanalerne som tranporterer væskerne og af sensorerne, der udfører analysen. Når størrelsen af disse anordninger når sub-micron område, taler vi om nanofluidics. Nanofluidics defineres som studiet af strømninger i og omkring nanoobjekter. Modellering af transport i nanofluidic systemer adskiller sig fra mikrofluid systemer, fordi ændringer inden for transport på grund af væggene bliver mere dominerende og vædsken består af færre molekyler. Kulstof-nanorør er rørformede grafit molekyler, som kan tænkes at fungere som nanoskala rør eller ledninger. Et andet vigtigt materiale til nanofluidics anvendelser er silica. I dag fremstilles silica nanokanaler i nanometer skalaen ved at anvende forskellige nanofabrikation teknikker. Silica nanonanokanaler bliver benyttet i flere nanoteknologiskeanvendelse såsom nanosensorer, nano separatorer, nanofilters og et antal anvendelserindenfor nanobiologi og biokemi. Eksperimenter på nanoskalaen er dyre og tidskrævende og iøvrigt kræver de transiente fænomener, som forbundet med flere nanoskala fænomener en meget høj tidslig opløsning af måleinstrumenterne. Numeriske beregninger indenfor nanofluidics er en lovende teknologi for grundlæggende studier, udvikling, og design af sådant udstyr. Numeriske beregninger supplerer eksperimentelle undersøgelser og giver en detaljeret rumlige og tidslig oplysninger om nanosystemet. Denne afhandling omhandler molekylær dynamiske beregning af grundlæggendenanoskala systemer. Arbejdet fokuserer på undersøgelser af transportmekanismer for vædsker og faste stoffer på nanoskala. Første del af afhandlingen giver en introduktion til molekylær dynamiske beregninger. Anden del præsenterer resultater fra tre forskellige forskningsprojekter. Første projekt omhandler et numerisk studie af termoforese, som en egnet mekanisme til at drive vanddr°aber gennem forskellige typer af kulstof nanorør. Resultaterne demonstrerer at vanddråber kan drives ved at påtrykke et termisk gradient langs nanorørerts akse og at hastigheden vokser med voksende termisk gradient. Det næste projekt omhandler en atomar analyse af en molekylær lineær motor fremstillet af ko-aksielle kulstofnanorør, som drives ved en termisk gradient. Molekylær dynamiske beregninger viser, at bevægelse af kapslen (det indre kulstof nanorør) kan kontrolleres af thermophoretic kræfter fremkaldt af termiske gradienter. Simuleringerne finde store terminale hastigheder på 100 til 400 nm/ns for pålagt termisk gradienter i intervallet af 1 til 3 K/nm. Desuden viser resultaterne, at dentermoforetiske kraft er hastighedsafhængige og dens størrelse reduceres ved øget hastighed. I sidste del af afhandlingen præsenteres en omfattende undersøgelse af nanoskala systemer bestående af vand og luft ved silica overflader, Denne undersøgelse omfatter kalibrering af de molekylær dynamiske kraftfelter til beskrivelse af silica-vand-luft interaktioner. Desuden foretages meget lang beregninger af nanoskala systemer, der indeholder silica, vand og luft. Lufts opløseligheden i vand undersøges ved forskellige tryk i silicavandsystemer. Beregningerne indikerer eksistens af et lag med høj luft koncentration tæt på silica overfladen. Endelig foretages beregninger af den tidlige fase af kapillar fyldning af silica nanokanaler. Fokus ved disse beregninger er lufts indflydelse på fyldningsprocessen, og undersøgelsen viser at luft ved højt tryk kan påvirke kapillaritet i silica kanaler.Nanotechnology and fluid mechanics are two scientific areas where recent progress has disclosed a variety of new posibilities. The advances in both fields stablished the grounds for interdisciplinary approaches and recent findings promise novel applications that are leading to a technological revolution. Novel nanofabrication techniques have opened up possibilities for the development of small-scale integrated devices, such as lab-on-a-chip for biochemical synthesis and analysis, the integration is achieved by miniaturization of the functional elements e.g., of the channels transporting the fluid and of the sensors performing the analysis, and as the size of these devices reaches the sub-micron range we enter the field of nanofluidics. Nanofluidics is defined as the study of flows in and around nanosized objects. Modeling of transport in nanofluidic systems differs from microfluidic systems because changes in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays,silica nanochannels are produced in nanometer scale using different nanofabrication techniques. Silica nanochannels are being implemented in several nanotechnology applications such as nanosensor devices, nano separators, nanofilters and a plethora of devices for nanobiological and biochemical applications. Experiments at the nanoscale are expensive and time consuming moreover the time scale associated to several nanoscale phenomena requires a very high time resolution of the devices performing nanoscale measurements. Computational nanofluidics is the enabling technology for fundamental studies, development, and design of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics methodology. In the second part of this thesis, we present the results of three different research projects. Fristly, wepresent a computational study of thermophoresis as a suitable mechanism to drive water droplets confined in different types of carbon nanotubes. We observe a motion of the water droplet in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate that the motion of the capsule (inner carbon nanotube) can be controlled by thermophoretic forces induced by thermal gradients. The simulations find large terminal velocities of 100 to 400 nmns−1 for imposed thermal gradients in the range of 1 to 3 Knm−1. Moreover, the results indicate that the thermophoretic force is velocity dependent and its magnitude decreases for increasing velocity. Finally, we present an extensive computational study of nanoscale systems including silica substrates and channels, water and air. This study includes the calibration of a force field to describe the silica-water-air interactions.Moreover, In this study we perform very long simulations of nanoscale systems containing silica, water and air. We investigate the solubility of air at different pressures in silica-water systems. From our simulations we infer a layer with high air density close to silica surface. Furthermore, we conduct simulations to analyze the earlier stage of the capillary filling process of silica nanochannels, we focus this study on the roll of air in this system. We find that air at high pressures can affect the capillarity in silica channels below 10 nm height.<br/