Bulk sediment parameter of three sediment cores from permafrost lowlands, Alaska Arctic Coastal Plain

Arctic lowland landscapes have been modified by thermokarst lake processes throughout the Holocene. Thermokarst lakes form as a result of ice-rich permafrost degradation and they may expand over time through thermal and mechanical shoreline erosion. We studied proximal and distal sedimentary records from a thermokarst lake located on the Arctic Coastal Plain of northern Alaska to reconstruct the impact of catchment dynamics and morphology on the lacustrine depositional environment and to quantify carbon accumulation in thermokarst lake sediments. Short cores were collected for analysis of pollen, sedimentological and geochemical proxies. Radiocarbon and Pb/Cs dating, as well as extrapolation of measured historic lake expansion rates, were applied to estimate a minimum lake age of ~ 1,400 calendar years BP. The pollen record is in agreement with the young lake age as it does not include evidence of the "alder high" that occurred in the region ~ 4.0 cal ka BP. The lake most likely initiated from a remnant pond in a drained thermokarst lake basin (DTLB) and deepened rapidly as evidenced by accumulation of laminated sediments. Increasing oxygenation of the water column as shown by higher Fe/Ti and Fe/S ratios in the sediment indicate shifts in ice regime with increasing water depth. More recently, the sediment source changed as the thermokarst lake expanded through lateral permafrost degradation, alternating from redeposited DTLB sediments, to increased amounts of sediment from eroding, older upland deposits, followed by a more balanced combination of both DTLB and upland sources. The characterizing shifts in sediment sources and depositional regimes in expanding thermokarst lakes were therefore archived in the thermokarst lake sedimentary record. This study also highlights the potential for Arctic lakes to recycle old carbon from thawing permafrost and thermokarst processes.

Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

Parameter space of experimental chaotic circuits with high-precision control parameters

The authors thank Professor Iber^e Luiz Caldas for the suggestions and encouragement. The authors F.F.G.d.S., R.M.R., J.C.S., and H.A.A. acknowledge the Brazilian agency CNPq and state agencies FAPEMIG, FAPESP, and FAPESC, and M.S.B. also acknowledges the EPSRC Grant Ref. No. EP/I032606/1.

Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction

In this paper we demonstrate the feasibility and utility of an augmented version of the Gibbs ensemble Monte Carlo method for computing the phase behavior of systems with strong, extremely short-ranged attractions. For generic potential shapes, this approach allows for the investigation of narrower attractive widths than those previously reported. Direct comparison to previous self-consistent Ornstein-Zernike approximation calculations is made. A preliminary investigation of out-of-equilibrium behavior is also performed. Our results suggest that the recent observations of stable cluster phases in systems without long-ranged repulsions are intimately related to gas-crystal and metastable gas-liquid phase separation.

Sea ice thickness distribution (ITD) Model for the Arctic, links to NetCDF files

Sea ice models contain many different parameterizations of which one of the most commonly used is a subgrid-scale ice thickness distribution (ITD). The effect of this model component and the associated ice strength formulation on the reproduction of observed Arctic sea ice is assessed. To this end the model's performance in reproducing satellite observations of sea ice concentration, thickness and drift is evaluated. For an unbiased comparison, different model configurations with and without an ITD are tuned with an automated parameter optimization. The original combination of ITD and ice strength parameterization does not lead to better results than a simple single category model. Yet changing to a simpler ice strength formulation, which depends linearly on the mean ice thickness across all thickness categories, allows to clearly improve the model-data misfit when using an ITD. In the original formulation, the ice strength depends strongly on the number of thickness categories, so that introducing more categories can lead to thicker albeit weaker ice on average.

Avoiding Overfitting in Inverse Modeling of Chloride Migration in Concrete

Inverse analysis for reactive transport of chlorides through concrete in the presence of electric field is presented. The model is solved using MATLAB’s built-in solvers “pdepe.m” and “ode15s.m”. The results from the model are compared with experimental measurements from accelerated migration test and a function representing the lack of fit is formed. This function is optimised with respect to varying amount of key parameters defining the model. Levenberg-Marquardt trust-region optimisation approach is employed. The paper presents a method by which the degree of inter-dependency between parameters and sensitivity (significance) of each parameter towards model predictions can be studied on models with or without clearly defined governing equations. Eigen value analysis of the Hessian matrix was employed to investigate and avoid over-parametrisation in inverse analysis. We investigated simultaneous fitting of parameters for diffusivity, chloride binding as defined by Freundlich isotherm (thermodynamic) and binding rate (kinetic parameter). Fitting of more than 2 parameters, simultaneously, demonstrates a high degree of parameter inter-dependency. This finding is significant as mathematical models for representing chloride transport rely on several parameters for each mode of transport (i.e., diffusivity, binding, etc.), which combined may lead to unreliable simultaneous estimation of parameters.

Physical model parameter optimisation for calibrated emulation of the Dallas Rangemaster Treble Booster guitar pedal

In this work we explore optimising parameters of a physical circuit model relative to input/output measurements, using the Dallas Rangemaster Treble Booster as a case study. A hybrid metaheuristic/gradient descent algorithm is implemented, where the initial parameter sets for the optimisation are informed by nominal values from schematics and datasheets. Sensitivity analysis is used to screen parameters, which informs a study of the optimisation algorithm against model complexity by fixing parameters. The results of the optimisation show a significant increase in the accuracy of model behaviour, but also highlight several key issues regarding the recovery of parameters.

High Pressure Speed of Sound and Related Thermodynamic Properties of 1-Alkyl-3-methylimidazolium Bis[(trifluoromethyl)sulfonyl]imides (from 1-Propyl- to 1-Hexyl-)

The knowledge of thermodynamic high-pressure speed of sound in ionic liquids (ILs) is a crucial way either to study the nature of the molecular interactions, structure and packing effects or to determine other key thermodynamic properties of ILs essential for their applications in any chemical and industrial processes. Herein, we report the speed of sound as a function temperature at pressures up to 101 MPa in four ultrapure ILs: 1-propyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-pentyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, and 1-hexyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, taking into consideration their relaxation behavior. Additionally, to further improve the reliability of the speed of sound results, the density, isentropic compressibility, and isobaric heat capacity as a function of temperature and pressure are calculated using an acoustic method.

Design and development of a diagonal-airflow batch dryer for spatial drying homogeneity

Das Verfahren der Lebensmitteltrocknung wird häufig angewendet, um ein Produkt für längere Zeit haltbar zu machen. Obst und Gemüse sind aufgrund ihres hohen Wassergehalts leicht verderblich durch biochemische Vorgänge innerhalb des Produktes, nicht sachgemäße Lagerung und unzureichende Transportmöglichkeiten. Um solche Verluste zu vermeiden wird die direkte Trocknung eingesetzt, welche die älteste Methode zum langfristigen haltbarmachen ist. Diese Methode ist jedoch veraltet und kann den heutigen Herausforderungen nicht gerecht werden. In der vorliegenden Arbeit wurde ein neuer Chargentrockner, mit diagonalem Luftstömungskanal entlang der Länge des Trocknungsraumes und ohne Leitbleche entwickelt. Neben dem unbestreitbaren Nutzen der Verwendung von Leitblechen, erhöhen diese jedoch die Konstruktionskosten und führen auch zu einer Erhöhung des Druckverlustes. Dadurch wird im Trocknungsprozess mehr Energie verbraucht. Um eine räumlich gleichmäßige Trocknung ohne Leitbleche zu erreichen, wurden die Lebensmittelbehälter diagonal entlang der Länge des Trockners platziert. Das vorrangige Ziel des diagonalen Kanals war, die einströmende, warme Luft gleichmäßig auf das gesamte Produkt auszurichten. Die Simulation des Luftstroms wurde mit ANSYS-Fluent in der ANSYS Workbench Plattform durchgeführt. Zwei verschiedene Geometrien der Trocknungskammer, diagonal und nicht diagonal, wurden modelliert und die Ergebnisse für eine gleichmäßige Luftverteilung aus dem diagonalen Luftströmungsdesign erhalten. Es wurde eine Reihe von Experimenten durchgeführt, um das Design zu bewerten. Kartoffelscheiben dienten als Trocknungsgut. Die statistischen Ergebnisse zeigen einen guten Korrelationskoeffizienten für die Luftstromverteilung (87,09%) zwischen dem durchschnittlich vorhergesagten und der durchschnittlichen gemessenen Strömungsgeschwindigkeit. Um den Effekt der gleichmäßigen Luftverteilung auf die Veränderung der Qualität zu bewerten, wurde die Farbe des Produktes, entlang der gesamten Länge der Trocknungskammer kontaktfrei im on-line-Verfahren bestimmt. Zu diesem Zweck wurde eine Imaging-Box, bestehend aus Kamera und Beleuchtung entwickelt. Räumliche Unterschiede dieses Qualitätsparameters wurden als Kriterium gewählt, um die gleichmäßige Trocknungsqualität in der Trocknungskammer zu bewerten. Entscheidend beim Lebensmittel-Chargentrockner ist sein Energieverbrauch. Dafür wurden thermodynamische Analysen des Trockners durchgeführt. Die Energieeffizienz des Systems wurde unter den gewählten Trocknungsbedingungen mit 50,16% kalkuliert. Die durchschnittlich genutzten Energie in Form von Elektrizität zur Herstellung von 1kg getrockneter Kartoffeln wurde mit weniger als 16,24 MJ/kg und weniger als 4,78 MJ/kg Wasser zum verdampfen bei einer sehr hohen Temperatur von jeweils 65°C und Scheibendicken von 5mm kalkuliert. Die Energie- und Exergieanalysen für diagonale Chargentrockner wurden zudem mit denen anderer Chargentrockner verglichen. Die Auswahl von Trocknungstemperatur, Massenflussrate der Trocknungsluft, Trocknerkapazität und Heiztyp sind die wichtigen Parameter zur Bewertung der genutzten Energie von Chargentrocknern. Die Entwicklung des diagonalen Chargentrockners ist eine nützliche und effektive Möglichkeit um dei Trocknungshomogenität zu erhöhen. Das Design erlaubt es, das gesamte Produkt in der Trocknungskammer gleichmäßigen Luftverhältnissen auszusetzen, statt die Luft von einer Horde zur nächsten zu leiten.