Life history trade-offs and community dynamics of small fishes in a seasonally pulsed wetland

We used a one-dimensional, spatially explicit model to simulate the community of small fishes in the freshwater wetlands of southern Florida, USA. The seasonality of rainfall in these wetlands causes annual fluctuations in the amount of flooded area. We modeled fish populations that differed from each other only in efficiency of resource utilization and dispersal ability. The simulations showed that these trade-offs, along with the spatial and temporal variability of the environment, allow coexistence of several species competing exploitatively for a common resource type. This mechanism, while sharing some characteristics with other mechanisms proposed for coexistence of competing species, is novel in detail. Simulated fish densities resembled patterns observed in Everglades empirical data. Cells with hydroperiods less than 6 months accumulated negligible fish biomass. One unique model result was that, when multiple species coexisted, it was possible for one of the coexisting species to have both lower local resource utilization efficiency and lower dispersal ability than one of the other species. This counterintuitive result is a consequence of stronger effects of other competitors on the superior species.

Fish population dynamics in a seasonally varying wetland

Small fishes in seasonally flooded environments such as the Everglades are capable of spreading into newly flooded areas and building up substantial biomass. Passive drift cannot account for the rapidity of observed population expansions. To test the ‘reaction–diffusion’ mechanism for spread of the fish, we estimated their diffusion coefficient and applied a reaction–diffusion model. This mechanism was also too weak to account for the spatial dynamics. Two other hypotheses were tested through modeling. The first—the ‘refuge mechanism’—hypothesizes that small remnant populations of small fishes survive the dry season in small permanent bodies of water (refugia), sites where the water level is otherwise below the surface. The second mechanism, which we call the ‘dynamic ideal free distribution mechanism’ is that consumption by the fish creates a prey density gradient and that fish taxis along this gradient can lead to rapid population expansion in space. We examined the two alternatives and concluded that although refugia may play an important role in recolonization by the fish population during reflooding, only the second, taxis in the direction of the flooding front, seems capable of matching empirical observations. This study has important implications for management of wetlands, as fish biomass is an essential support of higher trophic levels.

Self-healing of cracks during ductile regime machining of silicon: Insights from molecular dynamics simulation

During nanoindentation and ductile-regime machining of silicon, a phenomenon known as “self-healing” takes place in that the microcracks, microfractures, and small spallings generated during the machining are filled by the plastically flowing ductile phase of silicon. However, this phenomenon has not been observed in simulation studies. In this work, using a long-range potential function, molecular dynamics simulation was used to provide an improved explanation of this mechanism. A unique phenomenon of brittle cracking was discovered, typically inclined at an angle of 45° to 55° to the cut surface, leading to the formation of periodic arrays of nanogrooves being filled by plastically flowing silicon during cutting. This observation is supported by the direct imaging. The simulated X-ray diffraction analysis proves that in contrast to experiments, Si-I to Si-II (beta tin) transformation during ductile-regime cutting is highly unlikely and solid-state amorphisation of silicon caused solely by the machining stress rather than the cutting temperature is the key to its brittle-ductile transition observed during the MD simulations

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.

Discovery of relict subglacial lakes and their geometry and mechanism of drainage

Recent proxy measurements reveal that subglacial lakes beneath modern ice sheets periodically store and release large volumes of water, providing an important but poorly understood influence on contemporary ice dynamics and mass balance. This is because direct observations of how lake drainage initiates and proceeds are lacking. Here we present physical evidence of the mechanism and geometry of lake drainage from the discovery of relict subglacial lakes formed during the last glaciation in Canada. These palaeo-subglacial lakes comprised shallow (<10 m) lenses of water perched behind ridges orientated transverse to ice flow. We show that lakes periodically drained through channels incised into bed substrate (canals). Canals sometimes trend into eskers that represent the depositional imprint of the last high-magnitude lake outburst. The subglacial lakes and channels are preserved on top of glacial lineations, indicating long-term re-organization of the subglacial drainage system and coupling to ice flow.

Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes

Mevalonate pathway is of important clinical, pharmaceutical and biotechnological relevance. However, lack of the understanding of the phosphorylation mechanism of the kinases in this pathway has limited rationally engineering the kinases in industry. Here the phosphorylation reaction mechanism of a representative kinase in the mevalonate pathway, phosphomevalonate kinase, was studied by using molecular dynamics and hybrid QM/MM methods. We find that a conserved residue (Ser106) is reorientated to anchor ATP via a stable H-bond interaction. In addition, Ser213 located on the α-helix at the catalytic site is repositioned to further approach the substrate, facilitating the proton transfer during the phosphorylation. Furthermore, we elucidate that Lys101 functions to neutralize the negative charge developed at the β-, γ-bridging oxygen atom of ATP during phosphoryl transfer. We demonstrate that the dissociative catalytic reaction occurs via a direct phosphorylation pathway. This is the first study on the phosphorylation mechanism of a mevalonate pathway kinase. The elucidation of the catalytic mechanism not only sheds light on the common catalytic mechanism of GHMP kinase superfamily, but also provides the structural basis for engineering the mevalonate pathway kinases to further exploit their applications in the production of a wide range of fine chemicals such as biofuels or pharmaceuticals. 

Insight into the mechanism of galactokinase: role of a critical glutamate residue and helix/coil transitions

Galactokinase, the enzyme which catalyses the first committed step in the Leloir pathway, has attracted interest due to its potential as a biocatalyst and as a possible drug target in the treatment of type I galactosemia. The mechanism of the enzyme is not fully elucidated. Molecular dynamics (MD) simulations of galactokinase with the active site residues Arg-37 and Asp-186 altered predicted that two regions (residues 174-179 and 231-240) had different dynamics as a consequence. Interestingly, the same two regions were also affected by alterations in Arg-105, Glu-174 and Arg- 228. These three residues were identified as important in catalysis in previous computational studies on human galactokinase. Alteration of Arg-105 to methionine resulted in a modest reduction in activity with little change in stability. When Arg-228 was changed to methionine, the enzyme’s interaction with both ATP and galactose was affected. This variant was significantly less stable than the wild-type protein. Changing Glu-174 to glutamine (but not to aspartate) resulted in no detectable activity and a less stable enzyme. Overall, these combined in silico and in vitro studies demonstrate the importance of a negative charge at position 174 and highlight the critical role of the dynamics in to key regions of the protein. We postulate that these regions may be critical for mediating the enzyme’s structure and function. 

Nonlinear Dynamics Near the Cell Membrane of Chara Corallina

The phenomenon of patterned distribution of pH near the cell membrane of the algae Chara corallina upon illumination is well-known. In this paper, we develop a mathematical model, based on the detailed kinetic analysis of proton fluxes across the cell membrane, to explain this phenomenon. The model yields two coupled nonlinear partial differential equations which describe the spatial dynamics of proton concentration changes and transmembrane potential generation. The experimental observation of pH pattern formation, its period and amplitude of oscillation, and also its hysteresis in response to changing illumination, are all reproduced by our model. A comparison of experimental results and predictions of our theory is made. Finally, a mechanism for pattern formation in Chara corallina is proposed.

Coupling of Chemical Kinetics with Computational Fluid Dynamics in a Three-Dimensional Engine Model

The role of computer modeling has grown recently to integrate itself as an inseparable tool to experimental studies for the optimization of automotive engines and the development of future fuels. Traditionally, computer models rely on simplified global reaction steps to simulate the combustion and pollutant formation inside the internal combustion engine. With the current interest in advanced combustion modes and injection strategies, this approach depends on arbitrary adjustment of model parameters that could reduce credibility of the predictions. The purpose of this study is to enhance the combustion model of KIVA, a computational fluid dynamics code, by coupling its fluid mechanics solution with detailed kinetic reactions solved by the chemistry solver, CHEMKIN. As a result, an engine-friendly reaction mechanism for n-heptane was selected to simulate diesel oxidation. Each cell in the computational domain is considered as a perfectly-stirred reactor which undergoes adiabatic constant- volume combustion. The model was applied to an ideally-prepared homogeneous- charge compression-ignition combustion (HCCI) and direct injection (DI) diesel combustion. Ignition and combustion results show that the code successfully simulates the premixed HCCI scenario when compared to traditional combustion models. Direct injection cases, on the other hand, do not offer a reliable prediction mainly due to the lack of turbulent-mixing model, inherent in the perfectly-stirred reactor formulation. In addition, the model is sensitive to intake conditions and experimental uncertainties which require implementation of enhanced predictive tools. It is recommended that future improvements consider turbulent-mixing effects as well as optimization techniques to accurately simulate actual in-cylinder process with reduced computational cost. Furthermore, the model requires the extension of existing fuel oxidation mechanisms to include pollutant formation kinetics for emission control studies.

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

Data files to accompany the article in Nature Communications, in press.

Sensitisation waves in a bidomain fire-diffuse-fire model of intracellular Ca²⁺ dynamics

We present a bidomain threshold model of intracellular calcium (Ca²⁺) dynamics in which, as suggested by recent experiments, the cytosolic threshold for Ca²⁺ liberation is modulated by the Ca²⁺ concentration in the releasing compartment. We explicitly construct stationary fronts and determine their stability using an Evans function approach. Our results show that a biologically motivated choice of a dynamic threshold, as opposed to a constant threshold, can pin stationary fronts that would otherwise be unstable. This illustrates a novel mechanism to stabilise pinned interfaces in continuous excitable systems. Our framework also allows us to compute travelling pulse solutions in closed form and systematically probe the wave speed as a function of physiologically important parameters. We find that the existence of travelling wave solutions depends on the time scale of the threshold dynamics, and that facilitating release by lowering the cytosolic threshold increases the wave speed. The construction of the Evans function for a travelling pulse shows that of the co-existing fast and slow solutions the slow one is always unstable.

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.

Vortex Shedding Dynamics in Long Aspect-Ratio Aerodynamics Bodies

The focus of the current dissertation is to study qualitatively the underlying physics of vortex-shedding and wake dynamics in long aspect-ratio aerodynamics in incompressible viscous flow through the use of the KLE method. We carried out a long series of numerical experiments in the cases of flow around the cylinder at low Reynolds numbers. The study of flow at low Reynolds numbers provides an insight in the fluid physics and also plays a critical role when applying to stalled turbine rotors. Many of the conclusions about the qualitative nature of the physical mechanisms characterizing vortex formation, shedding and further interaction analyzed here at low Re could be extended to other Re regimes and help to understand the separation of the boundary layers in airfoils and other aerodynamic surfaces. In the long run, it aims to provide a better understanding of the complex multi-physics problems involving fluid-structure-control interaction through improved mathematical computational models of the multi-physics process. Besides the scientific conclusions produced, the research work on streamlined and bluff-body condition will also serve as a valuable guide for the future design of blade aerodynamics and the placement of wind turbines and hydrakinetic turbines, increasing the efficiency in the use of expensive workforce, supplies, and infrastructure. After the introductory section describing the main fields of application of wind power and hydrokinetic turbines, we describe the main features and theoretical background of the numerical method used here. Then, we present the analysis of the numerical experimentation results for the oscillatory regime right before the onset of vortex shedding for circular cylinders. We verified the wake length of the closed near-wake behind the cylinder and analysed the decay of the wake at the wake formation region, and then studied the St-Re relationship at the Reynolds numbers before the wake sheds compared to the experimental data. We found a theoretical model that describes the time evolution of the amplitude of fluctuations in the vorticity field on the twin vortex wake, which accurately matches the numerical results in terms of the frequency of the oscillation and rate of decay. We also proposed a model based on an analog circuit that is able to interpret the concerning flow by reducing the number of degrees of freedom. It follows the idea of the non-linear oscillator and resembles the dynamics mechanism of the closed near-wake with a common configured sine wave oscillator. This low-dimensional circuital model may also help to understand the underlying physical mechanisms, related to vorticity transport, that give origin to those oscillations.

Environmental Dynamics of Dissolved Black Carbon in Aquatic Ecosystems

Black carbon (BC), the incomplete combustion product from biomass and fossil fuel burning, is ubiquitously found in soils, sediments, ice, water and atmosphere. Because of its polyaromatic molecular characteristic, BC is believed to contribute significantly to the global carbon budget as a slow-cycling, refractory carbon pool. However, the mass balance between global BC generation and accumulation does not match, suggesting a removal mechanism of BC to the active carbon pool, most probable in a dissolved form. The presence of BC in waters as part of the dissolved organic matter (DOM) pool was recently confirmed via ultrahigh resolution mass spectrometry, and dissolved black carbon (DBC), a degradation product of charcoal, was found in marine and coastal environments. However, information on the loadings of DBC in freshwater environments and its global riverine flux from terrestrial systems to the oceans remained unclear. The main objectives of this study were to quantify DBC in diverse aquatic ecosystems and to determine its environmental dynamics. Surface water samples were collected from aquatic environments with a spatially significant global distribution, and DBC concentrations were determined by a chemical oxidation method coupled with HPLC detection. While it was clear that biomass burning was the main sources of BC, the translocation mechanism of BC to the dissolved phase was not well understood. Data from the regional studies and the developed global model revealed a strong positive correlation between DBC and dissolved organic carbon (DOC) dynamics, indicating a co-generation and co-translocation between soil OC and BC. In addition, a DOC-assistant DBC translocation mechanism was identified. Taking advantage of the DOC-DBC correlation model, a global riverine DBC flux to oceans on the order of 26.5 Mt C yr-1 (1 Mt = 1012 g) was determined, accounting for 10.6% of the global DOC flux. The results not only indicated that DOC was an important environmental intermediate for BC transfer and storage, but also provided an estimate of a major missing link in the global BC budget. The ever increasing DBC export caused by global warming will change the marine DOM quality and may have important consequences for carbon cycling in marine ecosystem.

Particle dynamics and airflow patterns in a ventilated two-zone enclosure

Understanding the transport mechanisms of aerosol particles in enclosures has broad ramifications in the context of cleaning strategies, and health risk assessment (e. g., occupational exposure). This paper addresses airflow pattern and aerosol transport mechanism in a ventilated two-zone enclosure with the outlet (exhaust location) situated at different locations. A numerical approach that combines a Eulerian simulation of turbulent flow with a Lagrangian particle-tracking algorithm is used. Simulations are carried out using solid suspensions with different sizes (1 to 100 micron) and densities (240 and 2300 kg/m3). The effect of location of the outlet (exhaust) on airflow patterns and aerosol dynamics is analyzed and quantified.