Development of coarse-grained models for the simulation of soft matter systems

This thesis aims to examine the parametrisation of coarse-grained models for the simulation of soft matter systems. The strengths and weaknesses of a range of methods are examined, and suggestions for improvements are made. Initially, two bottom-up methods, iterative Boltzmann inversion (IBI) and hybrid force matching (HFM) are applied to a liquid octane/benzene mixture and compared to a top-down model based on a version of statistical associating fluid theory, the SAFT-γ Mie equation of state. These models are tested for their ability to represent the structure and thermodynamics of the underlying atomistic system, as well as their transferability between temperatures and concentrations. Attempts are then made to address the poor transferability of the bottom-up models using a variant of IBI, multi-state IBI (MS-IBI). MS-IBI allows concentration transferable potentials to be generated but is not successful in improving temperature transferability. The state-point dependence of pair potentials is identified as the cause of poor temperature transferability, and initial attempts to address this are discussed. A range of coarse-grained models of the non-ionic liquid crystal TP6EO2M is examined. HFM is able to give a structurally accurate coarse-grained model; however, the difficulty of sampling all relevant configurations within an atomistic reference system appear to cause problems with calculating accurate association free energies. The new MARTINI 3 top-down force field is shown to improve upon the structural and thermodynamic properties of MARTINI 2, allowing larger system sizes to be studied. The nematic and hexagonal columnar chromonic phases are observed, and the concentration dependence seen in the experimental phase diagram is reproduced. This represents the first simulations of chromonic liquid crystal phases using systematic coarse graining

Shock induced formation of MgAl_2O_4 spinel from oxides

The physics of mineral grain sliding, which occurs upon dynamic compression of rocks, is investigated by shock loading single crystals of corundum (Al_2O_3) and periclase (MgO) in contact obliquely in impact experiments. Energy dispersive X-ray analysis and X-ray diffraction studies of samples recovered from 26–36 GPa, 800 ns experiments indicated that under certain conditions a spinel phase of composition MgAl_2O_4 and thickness ≤20 µm was produced at the interface between the two crystals. Although the computed shock (continuum) temperatures were below those necessary to melt the initial oxides, the spinel nonetheless appears to have formed as a result of localised melting, via grain boundary sliding friction, followed by rapid quenching. Scanning electron microscopy (SEM) revealed some evidence for such melting. Moreover, the timescale of the experiments is too short for solid state diffusion (during the shock state) to explain the observed spinel thickness, although defect enhanced solid state diffusion, subsequent to loading and unloading, remains a possibility. The results also reinforce other recent observations and theories of heterogeneous deformation in minerals

Moderate velocity oblique impact sliding: Production of shocked meteorite textures and palaeomagnetically important metallic spherules in planetary regoliths

We detail the production of metallic spherules in laboratory oblique shock impact experiments, and their applicability (1) to textures in a partly shock-melted chondritic meteorite and (2) to the occurrence of palaeomagnetically important fine iron or iron alloy particles in the lunar regolith. Samples recovered from 29–44 GPa, 800 ns, experiments revealed melting and textures reminiscent of metallic spherules in the Yanzhuang H-chondrite, including “dumbbell” forms and other more complex morphologies. Our experiments demonstrate that metallic spherules can be produced via oblique impact sliding at lower velocities (1.85 km s^(−1)) than are generally assumed in previous work associated with bulk-shock melting, and that oblique impact sliding is a viable mechanism for producing spherules in shock-induced veins in moderately shocked meteorites. Significantly, our experiments also produced fine metallic (iron alloy) spherules within the theoretical narrow size range (a few tens of nanometers for slightly ellipsoidal particles) for stable single-domain (SSD) particles, which are the most important palaeomagnetically, since they can record lunar and planetary magnetic fields over geological time periods. The experiments also produced spherules consistent with superparamagnetic (SP) and multidomain (MD) particle sizes. The fine SSD and SP particles on the lunar surface are currently thought to have been formed predominantly by space weathering processes. Our experiments suggest that oblique shock impact sliding may be a further means of producing the SSD and SP iron or iron alloy particles observed in the lunar regolith, and which are likely to occur in the regoliths of Mercury and other planetary bodies

Shock consolidation of diamond and graphite mixtures to fused polycrystalline diamond

The production of fused compacts of polycrystalline diamond was achieved by subjecting porous (35%–49% porosity) mixtures of diamond crystals plus graphite (13–16 wt. %) to dynamic shock pressures of 10–18 GPa. The recovered material from an initial mixture of 4–8-µm diamond crystals plus graphite revealed a very homogeneous texture with little evidence of original grain boundaries. The preconsolidation addition of graphite also allowed ultrafine (<5 µm) diamond crystals to be consolidated; this was not previously possible with the use of diamond crystals alone. The results are consistent with calculations which suggest that a thin layer of graphite surrounding a diamond crystal delays thermal equilibrium between the surface and interior of the diamond crystal, thus allowing greater surface heating. Consolidation is also probably enhanced by conversion of graphite to diamond, possibly via the liquid state

Atrazine Transport Within a Coastal Zone in Southeastern Puerto Rico: a Sensitivity Analysis of an Agricultural Field Model and Riparian Zone Management Model

Agrichemical runoff from farmland may adversely impact coastal water quality. Two models, the Agricultural Policy/Environmental eXtender (APEX) and the Riparian Ecosystem Management Model (REMM), were used to evaluate the movement of the herbicide atrazine to the Jobos Bay National Estuarine Research Reserve from adjacent fields. The reserve is located on Puerto Rico’s southeast coast. Edge-of-field atrazine outputs simulated with the APEX were routed through a grass-forest buffer using the REMM. Atrazine DT50 (half-life) values measured in both field and buffer soils indicated that accelerated degradation conditions had developed in the field soil due to repeated atrazine application. APEX simulations examined both the measured field and buffer soil atrazine DT50 and the model’s default value. The use of the measured field soil atrazine degradation rate in the APEX resulted in 33 % lower atrazine transport from the field. REMMsimulations indicated that the buffer system had the potential to reduce dissolved atrazine transport in surface runoff by 77%during non-tropical stormevents by increasing infiltration, slowing transport, and increasing time for pesticide degradation. During a large runoff event due to a tropical stormthat occurred close to the time of an atrazine application, the REMM simulated only a 37 % reduction in atrazine transport. The results indicate that large storm events soon after herbicide application likely dominate herbicide transport to coastal waters in the region. These results agree with water quality measurements in the reserve. This study demonstrated the sensitivity of these models to variations in DT50 values in evaluating atrazine fate and transport in the region and emphasizes that the use of measured DT50 values can improve model accuracy

Sixteen years of Collaborative Learning through Active Sense-making in Physics (CLASP) at UC Davis

This paper describes our large reformed introductory physics course at UC Davis, which bioscience students have been taking since 1996. The central feature of this course is a focus on sense-making by the students during the five hours per week discussion/labs in which the students take part in activities emphasizing peer-peer discussions, argumentation, and presentations of ideas. The course differs in many fundamental ways from traditionally taught introductory physics courses. After discussing the unique features of CLASP and its implementation at UC Davis, various student outcome measures are presented showing increased performance by students who took the CLASP course compared to students who took a traditionally taught introductory physics course. Measures we use include upper-division GPAs, MCAT scores, FCI gains, and MPEX-II scores.Comment: Also submitted to American Journal of Physic

BTS clinical statement for the diagnosis and management of ocular tuberculosis

The BTS clinical statement for the diagnosis and management of ocular tuberculosis (TB) draws on the expertise of both TB and and ophthalmic specialists to outline the current understanding of disease pathogenesis, diagnosis and management in adults. Published literature lacks high-quality evidence to inform clinical practice and there is also a paucity of data from animal models to elucidate mechanisms of disease. However, in order to improve and standardise patient care, this statement provides consensus points with the currently available data and agreed best practice

Scaling the gas transfer velocity and hydraulic geometry in streams and small rivers

Scaling is an integral component of ecology and earth science. To date, the ability to determine the importance of air–water gas exchange across large spatial scales is hampered partly by our ability to scale the gas transfer velocity and stream hydraulics. Here we report on a metadata analysis of 563 direct gas tracer release experiments that examines scaling laws for the gas transfer velocity. We found that the gas transfer velocity scales with the product of stream slope and velocity, which is in alignment with theory on stream energy dissipation. In addition to providing equations that predict the gas transfer velocity based on stream hydraulics, we used our hydraulic data set to report a new set of hydraulic exponents and coefficients that allow the prediction of stream width, depth, and velocity based on discharge. Finally, we report a new table of gas Schmidt number dependencies to allow researchers to estimate a gas transfer velocity using our equation for many gasses of interest