Relative free energies from nonequilibrium simulations: algorithms for determination of binding affinities, conformational states and phase transitions. Leading edge research will enable state of the art techniques in statistical mechanics to be applied to practical problems. All processes in biological, chemical and physical systems are governed by their free energy landscape, often only accessible computationally. This project will lead to an advanced tool for free energy calculation. Advanc ....Relative free energies from nonequilibrium simulations: algorithms for determination of binding affinities, conformational states and phase transitions. Leading edge research will enable state of the art techniques in statistical mechanics to be applied to practical problems. All processes in biological, chemical and physical systems are governed by their free energy landscape, often only accessible computationally. This project will lead to an advanced tool for free energy calculation. Advancement of emerging technologies in nanoscience, porous materials, membrane transport and drug design will benefit from this capability. The project therefore addresses the Priority Goal 'Breakthrough science'. A PhD student and an Early Career Research will be trained in research, gaining a range of valuable skills in theory and simulation. Read moreRead less
Fluctuations in the properties of nonequilibrium fluids and the influence of thermostatting mechanisms. The behaviour of nonequilibrium fluids will be studied by combining ideas from liquid state theory, statistical mechanics and dynamical systems theory. This work will result in development and testing of mathematical expressions (Fluctuation Theorems) that are consistent with the Second Law of Thermodynamics, which determines the direction of any change in any macroscopic system, but are also ....Fluctuations in the properties of nonequilibrium fluids and the influence of thermostatting mechanisms. The behaviour of nonequilibrium fluids will be studied by combining ideas from liquid state theory, statistical mechanics and dynamical systems theory. This work will result in development and testing of mathematical expressions (Fluctuation Theorems) that are consistent with the Second Law of Thermodynamics, which determines the direction of any change in any macroscopic system, but are also applicable to microscopic systems. The expressions will determine the probability that finite sized systems will violate the Second Law for small periods of time and will therefore contribute to development of a fundamental understanding of microscopic systems and the development of nanotechnology.
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Fluid properties and chaotic dynamics in equilibrium and nonequilibrium states. Over the last decade a revolution has been taking place in nonequilibrium statistical mechanics [Physics Today, Sept, 2002]. This revolution is characterized by adapting the mathematical theory of chaos to nonequilibrium statistical mechanics. Fundamental new theorems and algorithms for computing transport coefficients have been derived. The CIs have played a key role in this revolution. We seek to broaden these dev ....Fluid properties and chaotic dynamics in equilibrium and nonequilibrium states. Over the last decade a revolution has been taking place in nonequilibrium statistical mechanics [Physics Today, Sept, 2002]. This revolution is characterized by adapting the mathematical theory of chaos to nonequilibrium statistical mechanics. Fundamental new theorems and algorithms for computing transport coefficients have been derived. The CIs have played a key role in this revolution. We seek to broaden these developments by: generalizing a theorem which relates transport coefficients to chaoticity; detailed studies of the influence of thermostatting mechanisms on nonequilibrium chaoticity and fluctuations, and by understanding the range of applicability of a nonequilibrium fluctuation theorem for non-isoenergetic systems.Read moreRead less
Development of methodology for high throughput free energy calculations in drug design applications. The aim of the project is to develop a high throughput computational screening protocol for use in fragment-based drug design. The method will have universal applications to any plausible and available drug targets. The method will accelerate drug discovery on the targets associated with diabetes, obesity, dengue, skin cancer, etc., which are the primary disease focus of Australia. Australia as a ....Development of methodology for high throughput free energy calculations in drug design applications. The aim of the project is to develop a high throughput computational screening protocol for use in fragment-based drug design. The method will have universal applications to any plausible and available drug targets. The method will accelerate drug discovery on the targets associated with diabetes, obesity, dengue, skin cancer, etc., which are the primary disease focus of Australia. Australia as a whole and the University of Queensland in particular have invested heavily in various drug discovery programs, this will be of direct benefit to the ongoing research within Australia.Read moreRead less