Self-assembled monolayers studied by density-functional theory

Die vorliegende Dissertation widmet sich der quantenmechanischen Beschreibung der Adsorption selbstorganisierter monomolekularen Schichten (engl. self-assembled monolayers, SAMs) von einfachen Thiolen auf Übergangsmetalloberflchen. Für ab-initio Rechnungen auf den Computer-Clustern des Computational Materials Science (CMS) der Universität Wien wurde das Software-Paket VASP verwendet. Spontane Adsorption von Thiolen (wie z.B. Methanthiol, CH3SH) auf Metallobeflächen, vorwiegend Gold, wurde seit Anfang 1980 untersucht. Auf den meisten Metallen kommt es dann zu einer Bildung von Thiolaten (wie z.B. Methanthiolat, CH3S) schon bei niedrigen Temperaturen. In der vorliegenden Arbeit wurde die Adsorption von Methanthiol auf (111) kristallographischen Ebenen von Nickel, Palladium und Platin betrachtet. Als Modell der Oberflächenstruktur wurde eine 3D-Superzelle mit einer (√3×√3)R30° Periodizität des Adsorbats gewählt, da diese die dichteste und stabilste Packung der Moleküle auf der Oberfläche bildet. Dies entspricht einer Oberflächenbedeckung von 1/3. Ziel des Projektes war es, Trends in der Adsorptionsstärke von CH3SH und CH3S auf Oberflächen der Metalle der Ni–Gruppe zu untersuchen. Es wurde festgestellt, dass Methanthiol auf den Oberflächen schwach adsorbiert, wobei die Adsorptionsenergie in der Reihenfolge Ni<Pd<Pt zunimmt (−0.37/−0.60/−0.75 eV). Das Dissoziations-Produkt, Methanthiolat CH3S, bildet stark gebundene monomolekulare Schichten und die dabei freigegebene Adsorptionsenergie ist für alle 3 Metalle etwa gleich hoch (≈ −2.7 eV). Zusätzlich wurde eine detaillierte Schwingungsanalyse (Eigenwerte, Eigenvektoren und Intensitäten der infrarotaktiven Normalschwingungen) der adsorbierten Species durchgeführt und nachfolgend mit experimentellen Daten verglichen. Die elektronischen Zustände (projezierte Zustandsdichte-Spektren) und Ladungsdichte-Differenzen wurden ebenfalls dargestellt, um eine Charakterisierung der Adsorbat-Substrat Bindungen zu ermöglichen. Simulation der Wasserstoffatom-Dissoziation von adsorbiertem CH3SH (mit Hilfe der verbesserten Dimer-Methode) zeigte, dass die entsprechende Reaktionsbarriere in der Reihenfolge Ni<Pd<Pt (0/+0.18/+0.60 eV) zunimmt, während die Enthalpie dieses Reaktionsschrittes die umgekehrte Reihenfolge besitzt (−0.85/−0.52/−0.42 eV).The present thesis is devoted to the quantum-mechanical description of adsorption process and thermodynamics in self-assembled monolayers of simple thiols on transition metal surfaces. As an ab-initio computational tool, the VASP software package was used, and the calculations were performed on the computer clusters belonging to Computational Materials Science (CMS) framework at the University of Vienna. The adsorption of thiols (such as methane thiol, CH3SH) on metal surfaces, mostly gold, has been studied since early 1980’s. On most metals, formation of thiolates (like methane thiolate, CH3S) occurs already at moderate temperatures. In this thesis, the adsorption of methane thiol on the (111) crystallographic planes of nickel, palladium and platinum was studied in detail. As a model of the surface, a 3D-supercell with (√3×√3)R30° periodicity of the adsorbate has been chosen, as experimentally this is the most dense and stable packing of the molecules on the surface, giving a surface coverage of 1/3. The aim of this project was to investigate periodic trends in the strength of CH3SH adsorption and dissociation on the surfaces of the Ni-group metals. It was found out that methane thiol adsorbs weakly on the surfaces and the adsorption energy increases in the order Ni<Pd<Pt (−0.37/−0.60/−0.75 eV). Its dissociation product, methane thiolate CH3S, forms strongly bound monolayers and the released adsorption energy is almost the same for all 3 metals (≈ −2.7 eV). Vibrational properties (eigenvalues, eigenvectors and intensities of the infrared normal modes) of the adsorbed species have been thoroughly studied and subsequently compared with experimental data. The electronic states (projected density of states spectra) and difference charge-densities have been studied as well, leading to elucidation of the nature of adsorbate-substrate bonding. A simulation of the hydrogen dissociation from adsorbed CH3SH (using the very recently implemented improved dimer method) showed that the corresponding reaction barrier increases in the order Ni<Pd<Pt (0.00/+0.18/+0.60 eV), whereas the enthalpy of this reaction step follows a reverse order (−0.85/−0.52/−0.42 eV)

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample

Soleus Fiber Force and Maximal Shortening Velocity After Non-Weight Bearing with Intermittent Activity

This study examined the effectiveness of intermittent weight bearing (IWB) as a countermeasure to non-weight-bearing (NWB)-induced alterations in soleus type 1 fiber force (in mN), tension (P(sub o); force per fiber cross-sectional area in kN/sq m), and maximal unloaded shortening velocity (V(sub o), in fiber lengths/s). Adult rats were assigned to one of the following groups: normal weight bearing (WB), 14 days of hindlimb NWB (NWB group), and 14 days of hindlimb NWB with IWB treatments (IWB group). The IWB treatment consisted of four 10-min periods of standing WB each day. Single, chemically permeabilized soleus fiber segments were mounted between a force transducer and position motor and were studied at maximal Ca(2+) activation, after which type 1 fiber myosin heavy-chain composition was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. NWB resulted in a loss in relative soleus mass (-45%), with type 1 fibers displaying reductions in diameter (-28%) and peak isometric force (-55%) and an increase in V(sub o) (+33%). In addition, NWB induced a 16% reduction in type 1 fiber P., a 41% reduction in type 1 fiber peak elastic modulus [E(sub o), defined as ((delta)force/(delta)length x (fiber length/fiber cross-sectional area] and a significant increase in the P(sub o)/E(sub o) ratio. In contrast to NWB, IWB reduced the loss of relative soleus mass (by 22%) and attenuated alterations in type 1 fiber diameter (by 36%), peak force (by 29%), and V(sub o)(by 48%) but had no significant effect on P(sub o), E(sub o) or P(sub o)/E(sub o). These results indicate that a modest restoration of WB activity during 14 days of NWB is sufficient to attenuate type 1 fiber atrophy and to partially restore type 1 peak isometric force and V(sub o) to WB levels. However, the NWB-induced reductions in P(sub o) and E(sub o) which we hypothesize to be due to a decline in the number and stiffness of cross bridges, respectively, are considerably less responsive to this countermeasure treatment

Force-velocity-power and Force-pCa Relationships of Human Soleus Fibers After 17 Days of Bed Rest

Soleus muscle fibers from the rat display a reduction in peak power and Ca2+ sensitivity after hindlimb suspension. To examine human responses to non-weight bearing, we obtained soleus biopsies from eight adult men before and immediately after 17 days of bed rest (BR). Single chemically skinned fibers were mounted between a force transducer and a servo-controlled position motor and activated with maximal (isotonic properties) and/or submaximal (Ca2+ sensitivity) levels of free Ca2+. Gel electrophoresis indicated that all pre- and post-BR fibers expressed type I myosin heavy chain. Post-BR fibers obtained from one subject displayed increases in peak power and Ca2+ sensitivity. In contrast, post-BR fibers obtained from the seven remaining subjects showed an average 11% reduction in peak power (P \u3c 0.05), with each individual displaying a 7–27% reduction in this variable. Post-BR fibers from these subjects were smaller in diameter and produced 21% less force at the shortening velocity associated with peak power. However, the shortening velocity at peak power output was elevated 13% in the post-BR fibers, which partially compensated for their lower force. Post-BR fibers from these same seven subjects also displayed a reduced sensitivity to free Ca2+(P \u3c 0.05). These results indicate that the reduced functional capacity of human lower limb extensor muscles after BR may be in part caused by alterations in the cross-bridge mechanisms of contraction

Effects of perchlorate on the molecules of excitation-contraction coupling of skeletal and cardiac muscle

To understand the nature of the transmission process of excitation- contraction (EC) coupling, the effects of the anion perchlorate were investigated on the voltage sensor (dihydropyridine receptor, DHPR) and the Ca release channel (ryanodine receptor, RyR) of the sarcoplasmic reticulum (SR). The molecules, from rabbit skeletal muscle, were either separated in membrane vesicular fractions or biochemically purified so that the normal EC coupling interaction was prevented. Additionally, the effect of ClO4- was investigated on L-type Ca2+ channel gating currents of guinea pig ventricular myocytes, as a native DHPR not in the physiological interaction of skeletal muscle. At 20 mM, ClO4- had minor effects on the activation of ionic currents through Ca channels from skeletal muscle transverse tubular (T) membranes fused with planar bilayers: a +7-mV shift in the midpoint voltage, V, with no change in kinetics of activation or deactivation. This is in contrast with the larger, negative shift that ClO4- causes on the distribution of intramembrane charge movement of skeletal muscle. At up to 100 mM it did not affect the binding of the DHP [3H]PN200-110 to triad-enriched membrane fractions (TR). At 8 mM it did not affect the kinetics or the voltage distribution of gating currents of Ca channels in heart myocytes. These negative results were in contrast to the effects of ClO4- on the release channel. At 20 mM it increased several-fold the open probability of channels from purified RyR incorporated in planar bilayers and conducting Ba2+, an effect seen on channels first closed by chelation of Ca2+ or by the presence of Mg2+. It significantly increased the initial rate of efflux of 45Ca2+ from TR vesicles (by a factor of 1.75 at 20 mM and 4.5 at 100 mM). ClO4- also increased the binding of [3H]ryanodine to TR fractions. The relative increase in binding was 50-fold at the lowest [Ca2+] used (1 microM) and then decayed to much lower values as [Ca2+] was increased. The increase was due entirely to an increase in the association rate constant of ryanodine binding. The chaotropic ions SCN- and I- increased the association rate constant to a similar extent. The binding of ryanodine to purified RyR protein reconstituted into liposomes had a greater affinity than to TR fractions but was similarly enhanced by ClO4-. The reducing agent dithiothreitol (5 mM) did not reduce the effect of ClO4- , and 5% polyethylene glycol, with an osmolarity equivalent to 20 mM ClO4-, did not change ryanodine binding.(ABSTRACT TRUNCATED AT 400 WORDS

Dynamic Control of Nanoprecipitation in a Nanopipette

Studying the earliest stages of precipitation at the nanoscale is technically challenging but quite valuable as such phenomena reflect important processes such as crystallization and biomineralization. Using a quartz nanopipette as a nanoreactor, we induced precipitation of an insoluble salt to generate oscillating current blockades. The reversible process can be used to measure both kinetics of precipitation and relative size of the resulting nanoparticles. Counter ions for the highly water-insoluble salt zinc phosphate were separated by the pore of a nanopipette and a potential applied to cause ion migration to the interface. By analyzing the kinetics of pore blockage, two distinct mechanisms were identified: a slower process due to precipitation from solution, and a faster process attributed to voltage-driven migration of a trapped precipitate. We discuss the potential of these techniques in studying precipitation dynamics, trapping particles within a nanoreactor, and electrical sensors based on nanoprecipitation

The Influence of Food Intake Specificity in Children with Autism on Gut Microbiota

Autism spectrum disorder (ASD) is a complex of neurodevelopmental conditions with increasing incidence. The microbiota of children with ASD is distinct from neurotypical children, their food habits are also different, and it is known that nutrient intake influences microbiota in a specific way. Thus, this study investigates the food habits of children with ASD and their association with the gut microbiota. Children with ASD had their dietary energy intakes similar to controls, but they more often demonstrated food selectivity, which seemed to result in deficiency of micronutrients such as vitamins K, B6, C, iron, cooper, docosahexaenoic and docosapentanoic acid. Using high-throughput sequencing, a DNA library of intestinal microbiota was performed. Core microbiota was similar in children with and without ASD, but Dichelobacter, Nitriliruptor and Constrictibacter were found to be putative markers of ASD. The changes in gut microbiota that we observed in connection to food selectivity, intake of fats and omega-3 in particular, fermented milk products and animal/plant protein consumption had similar character, independent of diagnosis. However, high fibre intake was connected with a decreased &alpha;-diversity only in children with ASD. High carbohydrate and fibre intake influenced &beta;-diversity, changing the abundance of Bacteroides and other genera, many of them members of the Clostidiaceae. Modulating food habits of ASD children can influence their gut microbiota composition