Molecular computations for reactions and phase transitions: applications to protein stabilization, hydrates and catalysis

In this work we have made significant contributions in three different areas of interest: therapeutic protein stabilization, thermodynamics of natural gas clathrate-hydrates, and zeolite catalysis. In all three fields, using our various computational techniques, we have been able to elucidate phenomena that are difficult or impossible to explain experimentally. More specifically, in mixed solvent systems for proteins we developed a statistical-mechanical method to model the thermodynamic effects of additives in molecular-level detail. It was the first method demonstrated to have truly predictive (no adjustable parameters) capability for real protein systems. We also describe a novel mechanism that slows protein association reactions, called the “gap effect.” We developed a comprehensive picture of methioine oxidation by hydrogen peroxide that allows for accurate prediction of protein oxidation and provides a rationale for developing strategies to control oxidation. The method of solvent accessible area (SAA) was shown not to correlate well with oxidation rates. A new property, averaged two-shell water coordination number (2SWCN) was identified and shown to correlate well with oxidation rates. Reference parameters for the van der Waals Platteeuw model of clathrate-hydrates were found for structure I and structure II. These reference parameters are independent of the potential form (unlike the commonly used parameters) and have been validated by calculating phase behavior and structural transitions for mixed hydrate systems. These calculations are validated with experimental data for both structures and for systems that undergo transitions from one structure to another. This is the first method of calculating hydrate thermodynamics to demonstrate predictive capability for phase equilibria, structural changes, and occupancy in pure and mixed hydrate systems. We have computed a new mechanism for the methanol coupling reaction to form ethanol and water in the zeolite chabazite. The mechanism at 400°C proceeds via stable intermediates of water, methane, and protonated formaldehyde.

Flexure based mounts for sensitive payloads : a management and engineering study

by Daniel K. Moon.

Thermodynamics and log–contrast analysis in fluid geochemistry

There are two principal chemical concepts that are important for studying the natural environment. The first one is thermodynamics, which describes whether a system is at equilibrium or can spontaneously change by chemical reactions. The second main concept is how fast chemical reactions (kinetics or rate of chemical change) take place whenever they start. In this work we examine a natural system in which both thermodynamics and kinetic factors are important in determining the abundance of NH+4 , NO−2 and NO−3 in superficial waters. Samples were collected in the Arno Basin (Tuscany, Italy), a system in which natural and antrophic effects both contribute to highly modify the chemical composition of water. Thermodynamical modelling based on the reduction-oxidation reactions involving the passage NH+4 -> NO−2 -> NO−3 in equilibrium conditions has allowed to determine the Eh redox potential values able to characterise the state of each sample and, consequently, of the fluid environment from which it was drawn. Just as pH expresses the concentration of H+ in solution, redox potential is used to express the tendency of an environment to receive or supply electrons. In this context, oxic environments, as those of river systems, are said to have a high redox potential because O2 is available as an electron acceptor. Principles of thermodynamics and chemical kinetics allow to obtain a model that often does not completely describe the reality of natural systems. Chemical reactions may indeed fail to achieve equilibrium because the products escape from the site of the rection or because reactions involving the trasformation are very slow, so that non-equilibrium conditions exist for long periods. Moreover, reaction rates can be sensitive to poorly understood catalytic effects or to surface effects, while variables as concentration (a large number of chemical species can coexist and interact concurrently), temperature and pressure can have large gradients in natural systems. By taking into account this, data of 91 water samples have been modelled by using statistical methodologies for compositional data. The application of log–contrast analysis has allowed to obtain statistical parameters to be correlated with the calculated Eh values. In this way, natural conditions in which chemical equilibrium is hypothesised, as well as underlying fast reactions, are compared with those described by a stochastic approach

Experience in introduction of English terminology in engineering lessons: methodology and evaluation

This communication explains a experience for the introduction of English terminology in a technical degree of higher education. We present the methodology and assessment procedures used to evaluate the way the students perceived the introduction of terminology in English in two different subjects from 3rd and 5th year courses of a Computer Science degree in which English was not the vehicular language. We propose a strategy based on two main pillars, namely: 1) The design of materials, explanations, and exams, paying particular attention to the way in which the specific terminology was exposed to the students, and 2) The assessment of the impact in the students by means of the analysis of the feedback trough a set of enquiries. Our experience showed that the students responded very positively to the introduction of English terminology, and presented an affirmative feedback about the impact that an improvement of their linguistic abilities would have in their future work. Further, we present statistics regarding the use of English as the vehicular language for technical reports, which is envisaged as very useful by the students. Finally, we propose a set of questions for further debate which are centered in the role that English terminology should pay in technical degrees, and about the way in which universities should deploy resources in English languages within the different Syllabus

Engineering Foundation Year - Sustaining Success - Lecture 1 - slides

These materials are used in student tutorials as part of the routes to success course. The tutorials are typically delivered to a large group (~50) in an interactive manner, with the slides serving as reference/check materials. Some of the questions in the slides can also be used as individual handouts

The Higher Education Academy Engineering Subject Center

The engineering subject center provides support for engineering students and staff in higher education at university. The website provides articles helping students in a large range of subjects, such as book reviews for a variety subjects, support in writing reports or essays and personal development in subject areas and university life in general.

Engineering 1A

Exam questions and solutions for a first year engineering maths exam. Short questions (section A) and longer questions (section B). Diagrams for the question are all together in the support.zip file, as .eps files

Engineering 1B

Exercises and solutions for a first year course. Diagrams for the questions are all together in the support.zip file, as .eps files

Software Engineering Models

This presentation gives a high level introduction to modelling in software engineering. It looks in detail at how to model behaviour, in particular using UML Activity Diagrams.

Engineering Foundation Year - Sustaining Success Portfolio Template

Template - word processed document for 'Routes to Success' Coursework 3 'Sustaining Success'

Engineering Foundation Year - Sustaining Success Week 1

Slides for first week of teaching

Engineering Foundation Year - Sustaining Success Week 1

Slides for first week of teaching, PDF 6 up

Engineering Foundation Year - Sustaining Success Week 1

Slides for first week of teaching, PDF