In this work, the adsorption of protein on Au surface coated by self-assembled monolayers (SAMs) of alkanethiol chains is studied by molecular dynamics simulations with an all-atom model. Particularly, a more realistic embedded-atom method potential has been used to characterize the Au-Au interactions in the system as compared to previous studies. With this all-atom model, many experimental observations have been reproduced from the simulations. It is found that the SAMs have the lowest adsorption energy on Au (111) surface where the alkanethiol chains form a well-ordered (√3x√3) R30° triangular lattice at 300 K. Furthermore, it is confirmed that carboxyl-terminated SAMs are more effective to absorb proteins than the methyl-terminated SAMs. Base on the simulation results, we propose that the experimentally observed aggregation of protein-Au nanoparticle conjugates is mainly due to the electrostatic interactions between protein amino acids and carboxyl-terminated SAMs from multiple Au surfaces. / October 2016

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Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins. In particular, amphipathic α-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic α-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endo- and pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and themechanismof interaction it induces, as well asmolecular details of this process, still remain elusive. Lack of this knowledge is a key challenge in our efforts to elucidate some of the biological functions of membrane active peptides or to design peptides with tailored functionalities that can be exploited in drug delivery or antimicrobial strategies. In principle,molecular dynamics is a powerful research tool to study peptide-membrane interactions, which can provide a detailed description of these processes on molecular level. However, a model operating on the appropriate time and length scale is imperative in this description. In this study, we adopt a coarse-grained approach where the accessible simulation time and length scales reach microseconds and tens of nanometers, respectively. Thus, the two key objectives of this study are to validate the applicability of the adopted coarse-grained approach to the study of peptide-membrane interactions and to provide a systematic description of these interactions as a function of peptide structure and surface chemistry. We applied the adopted strategy to a range of peptide systems, whose behaviour has been well established in either experiments or detailed atomistic simulations and outlined the scope and applicability of the coarse-grained model. We generated some useful insights on the relationship between the structure of the peptides and themechanism of peptide-membrane interactions. Particularly interesting results have been obtained for LS3, a membrane spanning peptide, with a propensity to self-assembly into ion-conducting channels. Firstly, we captured, for the first time, the complete process of self-assembly of LS3 into a hexameric ion-conducting channel and explored its properties. The channel has structure of a barrel-stave pore with peptides aligned along the lipid tails. However, we discovered that a shorter version of the peptide leads to a more disordered, less stable structure often classified as a toroidal pore. This link between two types of pores has been established for the first time and opens interesting opportunities in tuning peptide structures for a particular pore-inducing mechanism. We also established that different classes of peptides can be uniquely characterized by the distinct energy profile as they cross the membrane. Finally, we extended this investigation to the internalization mechanisms of more complex entities such as peptide complexes and nanoparticles. Coarse-grained steered molecular dynamics simulations of these model systems are performed and some preliminary results are presented in this thesis. To summarize, in this thesis, we demonstrate that coarse-grained models can be successfully used to underpin peptide interaction and self-assembly processes in the presence of membranes in their full complexity. We believe that these simulations can be used to guide the design of peptides with tailored functionalities for applications such as drug delivery vectors and antimicrobial systems. This study also suggests that coarse-grained simulations can be used as an efficient way to generate initial configurations for more detailed atomistic simulations. These multiscale simulation ideas will be a natural future extension of this work.

Surface-only simulation methods for fluid dynamics are those that perform computation only on a surface representation, without relying on any volumetric discretization. Such methods have superior asymptotic complexity in time and memory than the traditional volumetric discretization approaches, and thus are more tractable for simulation of complex fluid phenomena. Although for most computer graphics applications and many engineering applications, the interior flow inside the fluid phases is typically not of interest, the vast majority of existing numerical techniques still rely on discretization of the volumetric domain. My research first tackles the mesh-based surface tracking problem in the multimaterial setting, and then proposes surface-only simulation solutions for two scenarios: the soap-films and bubbles, and the general 3D liquids. Throughout these simulation approaches, all computation takes place on the surface, and volumetric discretization is entirely eliminated.

Cellulose is a linear polysaccharide, serving as reinforcement in plant cell walls.Understanding its structure and properties is of importance in the developmentof nanostructured cellulose materials. The aim of this thesis is to address thisquestion by applying the computer simulation technique Molecular Dynamics(MD) onto an atomistic model of a native crystal form of cellulose.A molecular model of crystalline cellulose Iβ was developed and simulatedwith the GROMACS simulation software package.Temperature dependence of the crystal bulk model was investigated. A gradualtransition was observed between 350 K and 500 K in concordance with experimentalresults. The high temperature structure differed from the originalstructure in terms of crystal cell parameters, hydrogen bonding network andelastic modulus.Spin-lattice relaxation times, T1, from solid-state Nuclear Magnetic Resonancespectroscopy were compared with values calculated from the dynamics ofthe C4-H4 vector in MD simulations. Calculated T1 compared well with experimentallyobtained, suggesting well reproduced dynamics. Moreover, a differencein T1 of about a factor 2 was found for C4 atoms at surfaces parallel to differentcrystallographic planes. This supports a proposed explanation regarding anobserved doublet for C4 atoms in the NMR spectrum.Interaction energies between crystalline cellulose and water and 6− hydroxyhexanal(CL) were determined from simulations. Water was found to interactstronger with cellulose than CL. Moreover, the effect of grafting CL onto surfacecellulose chains was examined. For both water and CL interfaces, grafting ledto increased interaction. Electrostatic interactions were dominating in all cases,however grafting increased the importance of van der Waals interactions.The experimental approach to investigate polymer desorption by pulling itfrom a surface by the use of Atomic Force Microscopy (AFM) was enlightenedwith a modelling study. A single cellulose octamer was pulled from a cellulosecrystal into water and cyclohexane. Resulting pull-off energies proved a clearsolvent effect, 300 − 400 [kJ/mole] in cyclohexane and 100 − 200 [kJ/mole] inwater.In general, MD was shown to be useful when applied in combination withfeasible experimental techniques such as NMR and AFM to increase the fundamentalunderstanding of cellulose structure and properties. / Cellulosa förstärker cellväggen i växter i form av nanostrukturerade och mycketstarka fibriller. För utvecklingen av nya cellulosamaterial från dessa fibriller ären förståelse för cellulosans struktur och egenskaper viktig. Syftet med dennaavhandling är att med hjälp av en atomistisk modell och molekyldynamiskadatorsimuleringar (MD) öka kunskapen om cellulosa på atomär nivå.En atomistisk modell av kristallin cellulosa Iβ utvecklades och simuleradesmed simuleringsprogrampaketet GROMACS.Temperaturberoendet hos kristallin cellulosa i bulk undersöktes. Mellan350 K och 500 K skedde en gradvis kristallin strukturomvandling. Vid högre temperaturhade cellulosan annorlunda kristall-enhetscellsparametrar, vätebindingsmönsteroch elastisk modul jämfört med orginalstrukturen.Systemet cellulosa-vatten har stor praktisk betydelse. Spinn-gitter-relaxationstiderT1 beräknades därför från dynamiken hos C4-H4-vektorn i MD-simuleringaroch jämfördes med värden uppmätta med fastfas-NMR. De beräknadevärdena stämde väl överens med de experimentella och dynamiken vid ytan kanantas vara välreproducerad i modellen. Dessutom kunde en skillnad i T1 meden faktor 2 för C4-atomer på ytkedjor vid olika kristallografiska plan påvisas.Simuleringsresultaten stödjer därmed en tidigare föreslagen förklaring till endubblett för C4-atomer i cellulosans NMR-spektrum.Växelverkansenergier mellan cellulosa och polymeren PCL är intressant förnanokompositmaterial. Därför bestämdes växelverkansenergier mellan kristallincellulosa och vatten och cellulosa och 6-hydroxyhexanal (CL). Växelverkan mellancellulosa med vatten visade sig vara större än mellan cellulosa och CL.Ympning av CL-molekyler på cellulosaytan ledde till ökad växelverkan för såvälgränsytor mot vatten som mot CL. Elektrostatisk växelverkan dominerade vidsamtliga gränsytor, även om CL-ympning orsakade ökad andel av van der Waalskrafter.Polymerdesorption kan undersökas med hjälp av atomkraftmikroskopi (AFM).Ett simulerat experiment med MD utfördes därför genom att en cellulosaoktamerdrogs från en cellulosayta in i vatten eller cyklohexan. Det krävdes avsevärtmindre energi att dra loss oktameren i cyklohexan (300−400 kJ/mol) jämförtmed vatten (100 − 200 kJ/mol). Resultaten analyserades i termer av specifikväxelverkan mellan cellulosaoktameren och identifierbara kemiska grupper påcellulosaytan.MD har stor potential att öka förståelsen för cellulosa på molekylär nivå.MD-simuleringar kan inspirera experimentella mätningar genom upptäckter avnya fenomen. MD kan dessutom tillföra nya aspekter vid analys av experimentellaresultat. Det har i avhandlingen demonstrerats för metoder som NMR,AFM, mekanisk provning och mätning av termisk utvidgning / QC 20100621

By means of molecular dynamics simulation the effect of external direct current electric field on the polyethylene-like (PE-like) polymer and methyl chloride solvent system is investigated. Three systems include normal solution, dilute solution, and lower-density solution are simulated. For each system, four conditions include non-charged polymers in nonpolar solvents, non-charged polymers in polar solvents, charged polymers in nonpolar solvents, and charged polymer in polar solvents are simulated. The diffusion behavior of polymer in solvent is as functions of electric field, polarity of solvent molecules, and polarity of polymer. When an electric field is applied to the system include dielectric molecules, our calculation shows that the center of mass diffusion constant of polymer depends on the alignment of charged polymer or polar solvent molecules, the mobility of charged polymer or solvent molecules and the density of the system. The mobility of polar molecules results in the increase of the center of mass diffusion constant of polymer. The alignment of polar molecules results in the increase of fluid viscosity. This decreases the center of mass diffusion constant of polymer.

published_or_final_version / abstract / toc / Chemistry / Master / Master of Philosophy

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No description available.