With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin.
Until recently the idea that methods rooted in statistical physics could be used to elucidate phenomena and underlying mechanisms in biology and medicine was widely considered to be a distant dream. Elements of that dream are beginning to be realized, aided very considerably by machine learning and advances in measurement, exemplified by the development of large-scale biomedical data analysis for next-generation diagnostics. In this E-CAM interview of Tim Conrad, the growing importance of diagnostics in medicine and biology is discussed. One difficulty faced by such developments and shared with particle-based simulation is the “curse of dimensionality”. It is manifest in problems such as: (a) the use of a very large number of order parameters when trying to identify reaction mechanisms, nucleation pathways, metastable states, reaction rates; polymorph recognition (b) machine learning applied to electronic structure problems – such as neural network based potentials need very high dimensional basis sets; (c) systematic coarse-graining would ideally start with a very high dimensional space and systematically reduce the dimension. The opportunities and challenges for scientists engaging with industry are also discussed. Tim Conrad is Professor of “Medical Bioinformatics” at the Institute of Mathematics of the Free University of Berlin and head of MedLab, one of the four laboratories of the Modal research campus. MODAL is a public-private partnership project which conducts mathematical research on data-intensive modeling, simulation, and optimization of complex processes in the fields of energy, health, mobility, and communication. Tim Conrad is also the founder of three successful start-up companies.
In this E-CAM interview with Prof. Tim Conrad, the growing importance of diagnostics in medicine and biology is discussed, including concepts rooted in signal analysis relevant to systematic dimensional reduction, and pattern recognition, and the possibilities of their application to systematic coarse-graining. The opportunities and challenges for scientists of start-up companies are also discussed based on experience.
Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland
A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum universal gate is one of the major goals in the development of quantum computers. We have developed a software based on local control theory to design efficient state preparation control pulses for universal quantum gates which drive full population transfer between qubit states.
Dr. Hideki Kobayashi, Max-Planck-Institut für Polymerforschung, Germany
The ability to accurately determine and predict properties of newly developed polymer materials is highly important to researchers and industry, but at the same time represents a significant theoretical and computational challenge. We have developed a novel multiscale simulation method based on the hierarchical equilibration strategy, which significantly decreases the equilibrium properties calculation time while satisfying the thermodynamic consistency. A number of E-CAM modules was developed and implemented in he ESPResSo++ software package.
With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa
Interviewer: Dr. Donal Mackernan, University College Dublin
One quarter to one third of all proteins require metals to function but the description of metal ions in standard force fields is still quite primitive. In this case study and interview an E-CAM project to develop a suitable parameterisation using machine learning is described. The training scheme combines classical simulation with electronic structure calculations to produce a force field comprising standard classical force fields with additional terms for the metal ion-water and metal ion-protein interactions. The approach allows simulations to run as fast as standard molecular dynamics codes, and is suitable for efficient massive parallelism scale-up.
The power of advanced simulation combined with statistical theory , experimental know-how and high performance computing is used to design a protein based molecular switch sensor with remarkable sensitivity and significant industry potential. The sensor technology has applications across commercial markets including diagnostics, immuno-chemistry, and therapeutics.
With Prof. Christoph Dellago (CD), University of Vienna, and Dr. Donal Mackernan (DM), University College Dublin.
Recently there has been a dramatic increase in the use of machine learning in physics and chemistry, including its use to accelerate simulations of systems at an ab-initio level of accuracy, as well as for pattern recognition. It is now clear that these developments will significantly increase the impact of simulations on large scale systems requiring a quantum level of treatment, both for ground and excited states. These developments also lend themselves to simulations on massively parallel computing platforms, in many cases using classical simulation engines for quantum systems.
In the last few years, modelling of rare events has made tremendous progress and several computational methods have been put forward to study these events. Despite this effort, new approaches have not yet been included, with adequate efficiency and scalability, in common simulation packages. One objective of the Classical Dynamics Work Package of the project E-CAM is to close this gap. The present text is an easy-to-read article on the use of path sampling methods to study rare events, and the role of the OpenPathSampling package to performing these simulations. Practical applications of rare events sampling and scalabilities opportunities in OpenPathSampling are also discussed.
By Prof. David Ceperley, University of Illinois Urbana-Champaign
The computer simulation of electrons, atoms, molecules, and their assemblies in soft and hard matter is foundational for many scientific disciplines and important commercially. Exascale computing is coming and our community should take part as are our colleagues in lattice gauge theory, climate modeling, cosmology, genomics and other disciplines. Continue reading…
In many countries there is increasing demand for measurable socio-economic impact from academic research. Perhaps the UK is furthest down this path with a significant fraction of the funding for Universities dependent on the ‘Impact’ (defined as impact outside of academia) of the research performed . However much we might wish to ignore this trend, I am convinced that it will only increase, at least over the short to medium term. I also believe that, as a community, Continue reading…
By Prof. Giovanni Ciccotti, University of Rome La Sapienza
Numerical physics, i.e. numerical calculations serving the needs of traditional theoretical physics, exists at least since the times of Galileo, and probably long before. As Computer Simulation (started with solving problems in Statistical Mechanics), it exists only since the end of the second World War. It is based on the possibility of having computation speeds largely beyond human capabilities, even including speeds reachable by exploiting team work. Continue reading…