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Structure and informatics of the genetic code. Recent advances in biotechnology have seen its emergence as a highly
quantitative, numerically-based discipline. To exploit the available
data to the full will require, alongside computing power, new
analytical techniques. This project aims to develop such techniques,
by handling the systematics of the genetic code with methods derived
from theoretical physics and chemistry. Expected outcomes include a
dynamical (quantum field theory) model ....Structure and informatics of the genetic code. Recent advances in biotechnology have seen its emergence as a highly
quantitative, numerically-based discipline. To exploit the available
data to the full will require, alongside computing power, new
analytical techniques. This project aims to develop such techniques,
by handling the systematics of the genetic code with methods derived
from theoretical physics and chemistry. Expected outcomes include a
dynamical (quantum field theory) model of phylogenetic branching,
analyses of nucleic acid structure and content (spin chain models of
RNA binding and of DNA open reading frames), and insights into the
origin of the code itself (via numerical codon similarity measures).
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3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, ....3D Structure determination of biomacromolecular assemblies from sparse data. This project has direct impact on pharmaceutical research: Biomacromolecular interactions are key points for pharmaceutical intervention and detailed structural knowledge of dynamic protein interactions can significantly accelerate drug development. Australia has invested in expensive instrumentation that can be used with new laboratory methods to obtain information on delicately balanced biomacromolecular interactions, and how they malfunction in disease. This project will provide a computational framework to increase the impact of this investment by integrating measurements from a range of novel technologies and developing understanding of changes in structure of large protein complexes in different functional states.Read moreRead less
Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will c ....Theoretical Studies on the KcsA Potassium Channel and the L-type Calcium Channel. All electrical activities in the brain are regulated by opening and closing of ion channels. Thus, understanding their mechanisms is a fundamental problem in biology. The project is aimed at developing a theoretical model of two important types of ion channels. Using a supercomputer, we will first deduce the shape of the microstructure formed by a protein wall. Then, using a computer simulation technique, we will construct a set of physical models of biological ion channels, which will correctly replicate experimental observations. Such a theory will link the structure and function of an ion channel through the fundamental principles of physics.Read moreRead less
Entanglement renormalization: a new route to strongly correlated fermions and novel states of matter in two dimensions. The expected outcome of the research program is a significant boost in our understanding of strongly correlated fermion systems, which will reinforce Australia's competitiveness and international profile in aspects of breakthrough science and frontier technologies. By strengthening both the underpinning theory and innovative computational tools to study fermion systems, and by ....Entanglement renormalization: a new route to strongly correlated fermions and novel states of matter in two dimensions. The expected outcome of the research program is a significant boost in our understanding of strongly correlated fermion systems, which will reinforce Australia's competitiveness and international profile in aspects of breakthrough science and frontier technologies. By strengthening both the underpinning theory and innovative computational tools to study fermion systems, and by applying them to specific problems of recognized importance, this program will have direct implications in condensed matter physics and will exert significant influence in areas such as quantum chemistry, particle, nuclear and atomic physics, quantum computing, quantum atom optics and nanotechnology.Read moreRead less
GEOMETRIC NUMERICAL INTEGRATION. Many scientific phenomena in physics, astronomy, and chemistry, are modelled by ordinary differential equations (ODEs). Often these equations have no solution in closed form, and one relies on numerical integration. Traditionally this is done using Runge-Kutta methods or linear multistep methods. In the last decade, however, we (and others) have discovered novel classes of so-called "geometric" numerical integration methods that preserve qualititative featur ....GEOMETRIC NUMERICAL INTEGRATION. Many scientific phenomena in physics, astronomy, and chemistry, are modelled by ordinary differential equations (ODEs). Often these equations have no solution in closed form, and one relies on numerical integration. Traditionally this is done using Runge-Kutta methods or linear multistep methods. In the last decade, however, we (and others) have discovered novel classes of so-called "geometric" numerical integration methods that preserve qualititative features of certain ODE's exactly (in contrast to traditional methods), leading to crucial stability improvements. Extending concepts from dynamical systems theory and traditional numerical ODEs, this project will improve, extend and systematize this new field of geometric integration.Read moreRead less
Geometric Integration. This project gives an important boost to Australia's strength in the niche area of geometric numerical integration,in the face of strong international competition. It gathers 7 world experts from 5 countries to create new computer programs to improve calculations in dynamics, with applications ranging from astronomy, physics, chemistry, biology, and meteorology to finance. It strengthens Australia's links with the mathematical software industry, and will lead to world-clas ....Geometric Integration. This project gives an important boost to Australia's strength in the niche area of geometric numerical integration,in the face of strong international competition. It gathers 7 world experts from 5 countries to create new computer programs to improve calculations in dynamics, with applications ranging from astronomy, physics, chemistry, biology, and meteorology to finance. It strengthens Australia's links with the mathematical software industry, and will lead to world-class graduates and research training.Read moreRead less
Geometric numerical integration of differential equations. Differential equations (DEs) play a central role in modelling scientific phenomena in physics, biology, chemistry, astronomy, meteorology, and geoscience. We have developed new ways of solving DEs, using geometric integration, which have significant advantages over traditional methods because of the crucial nonlinear stability they provide.
This project, combining 7 world experts from 6 countries and 1 early career researcher, will pl ....Geometric numerical integration of differential equations. Differential equations (DEs) play a central role in modelling scientific phenomena in physics, biology, chemistry, astronomy, meteorology, and geoscience. We have developed new ways of solving DEs, using geometric integration, which have significant advantages over traditional methods because of the crucial nonlinear stability they provide.
This project, combining 7 world experts from 6 countries and 1 early career researcher, will place Australia at the forefront of this intensive international activity.
It will significantly strengthen Australia's links with the mathematical software industry (e.g. Wolfram Research, Inc), and will lead to world class graduates and research training.
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Special Research Initiatives - Grant ID: SR0354741
Funder
Australian Research Council
Funding Amount
$10,000.00
Summary
Quantum Many-Body Systems Network: Breakthrough Science and Frontier Technologies. This Initiative will bring together leading researchers with complementary expertise in mathematics and the enabling sciences to form a Network fostering world leading fundamental research and innovation in quantum many-body systems. The collaborative effort between mathematicians with powerful and sophisticated new techniques and physicists and chemists with deep insight into the challenges and opportunities of t ....Quantum Many-Body Systems Network: Breakthrough Science and Frontier Technologies. This Initiative will bring together leading researchers with complementary expertise in mathematics and the enabling sciences to form a Network fostering world leading fundamental research and innovation in quantum many-body systems. The collaborative effort between mathematicians with powerful and sophisticated new techniques and physicists and chemists with deep insight into the challenges and opportunities of the quantum realm will lead to breakthrough science of vital importance to the development of frontier technologies in Australia. This Network will also place a strong emphasis on research training, the mentoring of early career researchers and establishing collaborations with leading international research groups and networks.
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Robust Reformulation Methods. Many decision problems in engineering, business and economics are modeled as nonlinear continuous optimization problems. Often these are made difficult by the existence of constraints. In this project, we reformulate such problems as constrained nonsmooth equations, rather than optimization problems, and develop generalized Newton and quasi-Newton methods for solving them. The expected outcomes of this project include a systematic theory of reformulation methods, ....Robust Reformulation Methods. Many decision problems in engineering, business and economics are modeled as nonlinear continuous optimization problems. Often these are made difficult by the existence of constraints. In this project, we reformulate such problems as constrained nonsmooth equations, rather than optimization problems, and develop generalized Newton and quasi-Newton methods for solving them. The expected outcomes of this project include a systematic theory of reformulation methods, and robust and efficient algorithms for solving some important nonlinear continuous optimization problems. There is high potential for applications in engineering, business and finance.Read moreRead less
Quadratic Support Function Technique to Solving Hard Global Nonconvex Optimization Problems. Optimization techniques are becoming increasingly beneficial to modern Australian society in areas such as manufacturing and commerce by improving technical and management decisions. The proposed research is expected to produce enhanced optimization techniques that can be applied to solve a wider range of important problems too complex to be currently solved. The proposed research also represents an inte ....Quadratic Support Function Technique to Solving Hard Global Nonconvex Optimization Problems. Optimization techniques are becoming increasingly beneficial to modern Australian society in areas such as manufacturing and commerce by improving technical and management decisions. The proposed research is expected to produce enhanced optimization techniques that can be applied to solve a wider range of important problems too complex to be currently solved. The proposed research also represents an international collaboration which will improve Australia's ability to participate effectively in international research and innovation and to produce globally competitive mathematical technologiesRead moreRead less