EPSRC Research Software Engineer Fellowship Oliver Henrich
Lead Research Organisation:
University of Strathclyde
Department Name: Physics
Abstract
The interdisciplinary programme of research and software development I propose lies at the interface of physics, chemistry, and biology. Key target areas of this proposals, which my software will address, are coarse-grained modelling of DNA and RNA, the study of living systems and active matter far away from equilibrium, new soft energy and functional materials, enhanced encapsulation technologies and algorithms for new heterogeneous computing architectures.
The proposed software development programme aligns with a number of key areas of research that have been identified as Physics Grand Challenges. One of them is the understanding the physics of life. This has the goal to develop an integrating understanding of life from single molecules to whole biological systems. DNA and RNA are the two biopolymers that are involved in various biological roles, most notably in the encoding of the genetic instructions needed in the development and functioning of living organisms and gene transcription. Coarse-grained models of DNA or RNA can provide significant computational and conceptual advantages over atomistic models, leading often to three or more orders of magnitude greater efficiency. But they are not only an efficient alternative to atomistic models of DNA as they are indispensable for the modelling of DNA on timescales in the millisecond range and beyond, or when long DNA strands of tens of thousands of base pairs or more have to be considered. This is for instance important to study the dynamics of DNA supercoiling, the local over- or under-twisting of the double helix, which is important for gene expression.
Another Grand Challenge is the nanoscale design of functional material, which aims at engineering desired properties into the materials by using new principles rather than proceeding by trial and error. In the proposed programme I address different classes of functional and energy materials. One example are particle suspensions, which are fundamental in encapsulation technologies used in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or the micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new and highly promising avenue to more efficient, safer energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or the storage of renewable energy.
A third Grand Challenge is the emergence and physics far from thermodynamic equilibrium. As life itself is a process far away from equilibrium, the context of this research is also closely related to aspects of living matter and often challenges the classical theories of statistical physics.
The software that I will produce during this Fellowship will be open source and freely available for download from public repositories. Parts of it are likely to form later a key contribution to a highly optimised and standardised library of micro-, meso- and macroscale algorithms and a European infrastructure for the simulation of complex fluids. The software and research programme will be undertaken at the University of Edinburgh in collaboration with project partners at the University of Cambridge, the University of Oxford, University College London, the University of Barcelona, Spain and Sandia National Laboratories, USA.
The proposed software development programme aligns with a number of key areas of research that have been identified as Physics Grand Challenges. One of them is the understanding the physics of life. This has the goal to develop an integrating understanding of life from single molecules to whole biological systems. DNA and RNA are the two biopolymers that are involved in various biological roles, most notably in the encoding of the genetic instructions needed in the development and functioning of living organisms and gene transcription. Coarse-grained models of DNA or RNA can provide significant computational and conceptual advantages over atomistic models, leading often to three or more orders of magnitude greater efficiency. But they are not only an efficient alternative to atomistic models of DNA as they are indispensable for the modelling of DNA on timescales in the millisecond range and beyond, or when long DNA strands of tens of thousands of base pairs or more have to be considered. This is for instance important to study the dynamics of DNA supercoiling, the local over- or under-twisting of the double helix, which is important for gene expression.
Another Grand Challenge is the nanoscale design of functional material, which aims at engineering desired properties into the materials by using new principles rather than proceeding by trial and error. In the proposed programme I address different classes of functional and energy materials. One example are particle suspensions, which are fundamental in encapsulation technologies used in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or the micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new and highly promising avenue to more efficient, safer energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or the storage of renewable energy.
A third Grand Challenge is the emergence and physics far from thermodynamic equilibrium. As life itself is a process far away from equilibrium, the context of this research is also closely related to aspects of living matter and often challenges the classical theories of statistical physics.
The software that I will produce during this Fellowship will be open source and freely available for download from public repositories. Parts of it are likely to form later a key contribution to a highly optimised and standardised library of micro-, meso- and macroscale algorithms and a European infrastructure for the simulation of complex fluids. The software and research programme will be undertaken at the University of Edinburgh in collaboration with project partners at the University of Cambridge, the University of Oxford, University College London, the University of Barcelona, Spain and Sandia National Laboratories, USA.
Planned Impact
We are currently undergoing a transition to a new economy, which will be characterised by a deep and detailed understanding of the functioning mechanisms of DNA, RNA and their interaction with proteins. This transition will create new opportunities and industries and will have a transformative character on our societies, similar to that of the automotive, telecommunication and computer industry.
A concrete example of genetic technologies is genetically modified foods that have allowed for the introduction of new crop traits and far greater control over a food's genetic structure than previously afforded by traditional methods like selective breeding and mutation. An emerging example is personalised medicine, the customisation of healthcare using molecular analysis and a patient's genetic information for tailored gene therapies and medical decisions. The fundamental insights that my software will enable will undoubtedly create opportunities for improvement and enhancement of the two above mentioned, well-established applications of genetic technologies and open up completely new possibilities.
Recently, non-biological applications such as DNA-nanotechnology have sparked great interest, and the sequence-specific coarse-grained models for DNA and RNA are directly targeting this field. DNA origami for example is the programmable bottom-up approach of designing nanoscale materials and two- and three-dimensional shapes in a self-assembled manner by using the specificity of the interaction between complementary base pairs. There is great desire among experimentalists to get a computational feedback that is needed to reduce the financial cost and time required to design nanoscale self-assembled materials. Coarse-grained DNA models are the only candidates that could fill this technological gap.
The nanoscale design of new functional soft materials is another focus of this proposal. Particle suspensions are fundamentally important for encapsulation technologies in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new avenue to more efficient energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or storage of renewable energy. But before these insights can be turned into a competitive advantage for our industrial collaborators a detailed understanding of the behaviour of these systems needs to be first acquired. This can only be achieved through accurate descriptions of the complex morphology and dynamics of their different constituents, which my software will enable.
The field of active matter is very new and burgeoning with novel scientific insights that challenge the traditional beliefs of statistical physics and sometimes constitute new physics. The consequences of this are rather profound and can only be probed by a body of numerical simulations that account for all non-linearities and couplings in the underlying equations of motion.
While the software that I will develop is essential for the research community of computational soft matter and biological physics, the impact of the research originating from this software will often go beyond academia. I envisage its use will extend to many other communities. I anticipate that engineers, material scientists, physical chemists, biochemists, cell or molecular biologists as well as workers in industry are likely to engage in the future with many of the codes which I will provide. The software will be open source and also form an essential contribution to a future European infrastructure for the simulation of complex fluids.
A concrete example of genetic technologies is genetically modified foods that have allowed for the introduction of new crop traits and far greater control over a food's genetic structure than previously afforded by traditional methods like selective breeding and mutation. An emerging example is personalised medicine, the customisation of healthcare using molecular analysis and a patient's genetic information for tailored gene therapies and medical decisions. The fundamental insights that my software will enable will undoubtedly create opportunities for improvement and enhancement of the two above mentioned, well-established applications of genetic technologies and open up completely new possibilities.
Recently, non-biological applications such as DNA-nanotechnology have sparked great interest, and the sequence-specific coarse-grained models for DNA and RNA are directly targeting this field. DNA origami for example is the programmable bottom-up approach of designing nanoscale materials and two- and three-dimensional shapes in a self-assembled manner by using the specificity of the interaction between complementary base pairs. There is great desire among experimentalists to get a computational feedback that is needed to reduce the financial cost and time required to design nanoscale self-assembled materials. Coarse-grained DNA models are the only candidates that could fill this technological gap.
The nanoscale design of new functional soft materials is another focus of this proposal. Particle suspensions are fundamentally important for encapsulation technologies in consumer products like foods, beverages, cleaning agents, personal care products, paints and inks or in the petrochemical industry or micro-technological sector with lab-on-a-chip devices. Nanostructured charged soft materials are a new avenue to more efficient energy producing or storing devices and have great potential to fill technological gaps in the design of batteries and electrodes or storage of renewable energy. But before these insights can be turned into a competitive advantage for our industrial collaborators a detailed understanding of the behaviour of these systems needs to be first acquired. This can only be achieved through accurate descriptions of the complex morphology and dynamics of their different constituents, which my software will enable.
The field of active matter is very new and burgeoning with novel scientific insights that challenge the traditional beliefs of statistical physics and sometimes constitute new physics. The consequences of this are rather profound and can only be probed by a body of numerical simulations that account for all non-linearities and couplings in the underlying equations of motion.
While the software that I will develop is essential for the research community of computational soft matter and biological physics, the impact of the research originating from this software will often go beyond academia. I envisage its use will extend to many other communities. I anticipate that engineers, material scientists, physical chemists, biochemists, cell or molecular biologists as well as workers in industry are likely to engage in the future with many of the codes which I will provide. The software will be open source and also form an essential contribution to a future European infrastructure for the simulation of complex fluids.
Organisations
- University of Strathclyde (Fellow, Lead Research Organisation)
- UNIVERSITY OF OXFORD (Collaboration)
- Swiss Federal Institute of Technology in Lausanne (EPFL) (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- Sapienza University of Rome (Collaboration)
- Ca' Foscari University of Venice (Collaboration)
- Arizona State University (Collaboration)
- UNIVERSITY OF YORK (Collaboration)
- Sandia Laboratories (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
People |
ORCID iD |
Oliver O Henrich (Principal Investigator / Fellow) |
Publications
Henrich O
(2017)
The secret of the blue fog
in Physics World
Fujii S
(2021)
Shear-enhanced elasticity in the cubic blue phase I.
in Physical review. E
Fujii S
(2018)
Shear-enhanced elasticity in the cubic blue phase I
Schiller UD
(2017)
Mesoscopic modelling and simulation of soft matter.
in Soft matter
Schiller U
(2017)
Mesoscopic Modelling and Simulation of Soft Matter
Bianco S
(2022)
Heterogeneous migration routes of DNA triplet repeat slip-outs.
in Biophysical reports
Foglino M
(2017)
Flow of Deformable Droplets: Discontinuous Shear Thinning and Velocity Oscillations.
in Physical review letters
Xie J
(2019)
Effective mean free path and viscosity of confined gases
in Physics of Fluids
Lesniewska M
(2022)
Controllable particle migration in liquid crystal flows.
in Soft matter
Description | The LAMMPS implementation of oxDNA is now firmly among the two software distributions of the oxDNA coarse-grained DNA and RNA model and is used by dozens of groups around the world. With its shared memory parallelisation for CPU-architectures it is particularly useful for studying smaller to medium-sized systems in the range of 10,000 base pairs. |
Exploitation Route | The LAMMPS implementation will become the main MD implementation of the oxDNA and oxRNA models and is already used by a growing global community that comprises more than 30 groups around the World. The outcome of this project is the starting point for DNA simulation on the exascale. This will be realised through porting of the oxDNA LAMMPS interaction styles to KOKKOS-style packages, which are supported any GPU and CPU compute architecture. |
Sectors | Digital/Communication/Information Technologies (including Software) Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
URL | https://www.lammps.org |
Description | Our coarse-grained DNA and RNA models and software have now been used in hundreds of publications, and we still monitor a steep increase in utilisation of the oxDNA model. However, it is beyond the scope of this report here to track how our model and software has created practical impact as this is one step removed from our work. |
First Year Of Impact | 2018 |
Sector | Education,Healthcare,Pharmaceuticals and Medical Biotechnology |
Impact Types | Societal Economic Policy & public services |
Description | oxDNA3 - Introducing Sequence-Specific Curvature And Elasticity Into A Coarse-Grained DNA Model |
Amount | £540,000 (GBP) |
Funding ID | EP/V06231X/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2022 |
End | 06/2025 |
Title | Enhancement of post-processing and visualisation |
Description | The suite of tools and converters for oxDNA (tacoxDNA) has been extended to process trajectories in LAMMPS data format and convert them into native oxDNA data format. This enables us to use and contribute to the development of the new bespoke visualisation tool oxView introduced by Petr Sulc, Arizona State University, USA. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | LAMMPS trajectories can be converted in native oxDNA format. This allows to switch between LAMMPS and the oxDNA standalone code back and forth, thereby drawing on their extensive range of bespoke functionality, e.g. advanced molecular dynamics and sampling tools like meta dynamics and Monte Carlo methods. Another impact of this conversion tool is that oxView can be used for visualisation of LAMMPS trajectories. This gives a far superior representation of the DNA / RNA conformations and relative orientation of backbone and base. |
URL | http://tacoxdna.sissa.it |
Title | Implementation of the oxDNA2 and oxRNA model |
Description | The implementation of the oxDNA model has been now extended to include the upgraded oxDNA2 model and the oxRNA model, the coarse-grained model for RNA. All software is available from the central LAMMPS repository at Sandia National Laboratories, USA. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | We notice an increasing interest in the LAMMPS implementation of the oxDNA and oxRNA models. During the first oxDNA user and developer workshop in September 2019 it was decided that the LAMMPS implementation will become the main molecular dynamics implementation. |
Title | LAMMPS implementation of the oxDNA model |
Description | The oxDNA model is now available through the LAMMPS code, which is a community code for molecular dynamics simulations |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | It is too early to state any concrete impact. However, I had a few requests from the UK, Europe and the USA about the usage of this implementation, etc. |
URL | http://lammps.sandia.gov/doc/Section_packages.html#user-cgdna-package |
Title | Performance improvements of CG-DNA package in LAMMPS |
Description | A 20% performance increase was achieved by refactoring force calculation routines. Unit tests have been added to ensure robustness of newly developed functionality. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | The LAMMPS code is used by 1000s of researchers worldwide. The CG-DNA package is used by dozens of groups. |
URL | https://www.lammps.org |
Description | Dynamics of triplet-repeat sequences |
Organisation | University of Glasgow |
Department | School of Chemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We provide simulation and modelling expertise to interpret and analyse experimental data. |
Collaborator Contribution | Our collaborator provides experimental data. |
Impact | We have one publication. |
Start Year | 2020 |
Description | Implementation of the oxDNA model into the LAMMPS code |
Organisation | Arizona State University |
Country | United States |
Sector | Academic/University |
PI Contribution | The implementation was carried out by myself. I was also the lead scientist on a documenting article about this implementation. |
Collaborator Contribution | Dr Thomas E. Ouldridge (Imperial College London) helped with the implementation and verification of the code for the oxDNA model and provided consulting services for applications. The collaboration has been now extended to Dr Lorenzo Rovigatti (La Sapienza) and Dr Flavio Romano (Ca' Foscari University of Venice), who assisted with the implementation of the upgraded oxDNA2 model. Dr Petr Sulc (Arizona State University) provided consultancy services for the implementation of oxRNA, the coarse-grained model of RNA. |
Impact | The oxDNA model has been implemented into the LAMMPS code and is available for download from the central LAMMPS repository. This has been extended to include the oxDNA2 model and the oxRNA model. This collaboration is superseded by a wider network collaboration that involves as well researchers at EPF Lausanne, Switzerland and at the University of Oxford, UK. |
Start Year | 2016 |
Description | Implementation of the oxDNA model into the LAMMPS code |
Organisation | Ca' Foscari University of Venice |
Country | Italy |
Sector | Academic/University |
PI Contribution | The implementation was carried out by myself. I was also the lead scientist on a documenting article about this implementation. |
Collaborator Contribution | Dr Thomas E. Ouldridge (Imperial College London) helped with the implementation and verification of the code for the oxDNA model and provided consulting services for applications. The collaboration has been now extended to Dr Lorenzo Rovigatti (La Sapienza) and Dr Flavio Romano (Ca' Foscari University of Venice), who assisted with the implementation of the upgraded oxDNA2 model. Dr Petr Sulc (Arizona State University) provided consultancy services for the implementation of oxRNA, the coarse-grained model of RNA. |
Impact | The oxDNA model has been implemented into the LAMMPS code and is available for download from the central LAMMPS repository. This has been extended to include the oxDNA2 model and the oxRNA model. This collaboration is superseded by a wider network collaboration that involves as well researchers at EPF Lausanne, Switzerland and at the University of Oxford, UK. |
Start Year | 2016 |
Description | Implementation of the oxDNA model into the LAMMPS code |
Organisation | Imperial College London |
Department | Department of Bioengineering |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | The implementation was carried out by myself. I was also the lead scientist on a documenting article about this implementation. |
Collaborator Contribution | Dr Thomas E. Ouldridge (Imperial College London) helped with the implementation and verification of the code for the oxDNA model and provided consulting services for applications. The collaboration has been now extended to Dr Lorenzo Rovigatti (La Sapienza) and Dr Flavio Romano (Ca' Foscari University of Venice), who assisted with the implementation of the upgraded oxDNA2 model. Dr Petr Sulc (Arizona State University) provided consultancy services for the implementation of oxRNA, the coarse-grained model of RNA. |
Impact | The oxDNA model has been implemented into the LAMMPS code and is available for download from the central LAMMPS repository. This has been extended to include the oxDNA2 model and the oxRNA model. This collaboration is superseded by a wider network collaboration that involves as well researchers at EPF Lausanne, Switzerland and at the University of Oxford, UK. |
Start Year | 2016 |
Description | Implementation of the oxDNA model into the LAMMPS code |
Organisation | Sapienza University of Rome |
Country | Italy |
Sector | Academic/University |
PI Contribution | The implementation was carried out by myself. I was also the lead scientist on a documenting article about this implementation. |
Collaborator Contribution | Dr Thomas E. Ouldridge (Imperial College London) helped with the implementation and verification of the code for the oxDNA model and provided consulting services for applications. The collaboration has been now extended to Dr Lorenzo Rovigatti (La Sapienza) and Dr Flavio Romano (Ca' Foscari University of Venice), who assisted with the implementation of the upgraded oxDNA2 model. Dr Petr Sulc (Arizona State University) provided consultancy services for the implementation of oxRNA, the coarse-grained model of RNA. |
Impact | The oxDNA model has been implemented into the LAMMPS code and is available for download from the central LAMMPS repository. This has been extended to include the oxDNA2 model and the oxRNA model. This collaboration is superseded by a wider network collaboration that involves as well researchers at EPF Lausanne, Switzerland and at the University of Oxford, UK. |
Start Year | 2016 |
Description | Implementation of the oxDNA model into the LAMMPS code |
Organisation | University of Oxford |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | The implementation was carried out by myself. I was also the lead scientist on a documenting article about this implementation. |
Collaborator Contribution | Dr Thomas E. Ouldridge (Imperial College London) helped with the implementation and verification of the code for the oxDNA model and provided consulting services for applications. The collaboration has been now extended to Dr Lorenzo Rovigatti (La Sapienza) and Dr Flavio Romano (Ca' Foscari University of Venice), who assisted with the implementation of the upgraded oxDNA2 model. Dr Petr Sulc (Arizona State University) provided consultancy services for the implementation of oxRNA, the coarse-grained model of RNA. |
Impact | The oxDNA model has been implemented into the LAMMPS code and is available for download from the central LAMMPS repository. This has been extended to include the oxDNA2 model and the oxRNA model. This collaboration is superseded by a wider network collaboration that involves as well researchers at EPF Lausanne, Switzerland and at the University of Oxford, UK. |
Start Year | 2016 |
Description | LAMMPS code development |
Organisation | Sandia Laboratories |
Country | United States |
Sector | Private |
PI Contribution | I develop and maintain the CG-DNA package within the LAMMPS code. |
Collaborator Contribution | Support and advice via email |
Impact | The code is released through the central LAMMPS repository. The latest contribution is for the Stable Release Summer 2022 and includes performance enhancements. |
Start Year | 2017 |
Description | University of York, Physics of Life Group |
Organisation | University of York |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We provide coarse-grained DNA modelling competence for studies on DNA supercoiling. |
Collaborator Contribution | Our partners at the University of York, Dr Agnes Noy and Prof Mark Leake, provide expertise in atomistic DNA modelling and experimental methods. |
Impact | This new collaboration is at an early stage and there are no concrete outputs as of March 2021 in form of publications. However, two BSc theses are currently in progress and these will be continued during MSc projects next year. The collaboration is multi-disciplinary and involves biophysics and the life sciences. |
Start Year | 2019 |
Description | oxDNA Developer Network |
Organisation | Imperial College London |
Department | Department of Bioengineering |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | This collaboration works towards the next generation of oxDNA model, which will include sequence-specific curvature and elasticity. I am coordinating these activities, lead the development and am responsible for implementations into the LAMMPS code. |
Collaborator Contribution | Prof John H. Maddocks seconds a PhD student. |
Impact | We are currently in the process of applying for funding. The collaboration involves the disciplines of applied mathematics, (bio-)physics, (bio-)chemistry and includes aspects of research software engineering. |
Start Year | 2020 |
Description | oxDNA Developer Network |
Organisation | Swiss Federal Institute of Technology in Lausanne (EPFL) |
Country | Switzerland |
Sector | Public |
PI Contribution | This collaboration works towards the next generation of oxDNA model, which will include sequence-specific curvature and elasticity. I am coordinating these activities, lead the development and am responsible for implementations into the LAMMPS code. |
Collaborator Contribution | Prof John H. Maddocks seconds a PhD student. |
Impact | We are currently in the process of applying for funding. The collaboration involves the disciplines of applied mathematics, (bio-)physics, (bio-)chemistry and includes aspects of research software engineering. |
Start Year | 2020 |
Description | oxDNA Developer Network |
Organisation | University of Oxford |
Department | Department of Chemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | This collaboration works towards the next generation of oxDNA model, which will include sequence-specific curvature and elasticity. I am coordinating these activities, lead the development and am responsible for implementations into the LAMMPS code. |
Collaborator Contribution | Prof John H. Maddocks seconds a PhD student. |
Impact | We are currently in the process of applying for funding. The collaboration involves the disciplines of applied mathematics, (bio-)physics, (bio-)chemistry and includes aspects of research software engineering. |
Start Year | 2020 |
Description | oxDNA Developer Network |
Organisation | University of Oxford |
Department | Department of Physics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | This collaboration works towards the next generation of oxDNA model, which will include sequence-specific curvature and elasticity. I am coordinating these activities, lead the development and am responsible for implementations into the LAMMPS code. |
Collaborator Contribution | Prof John H. Maddocks seconds a PhD student. |
Impact | We are currently in the process of applying for funding. The collaboration involves the disciplines of applied mathematics, (bio-)physics, (bio-)chemistry and includes aspects of research software engineering. |
Start Year | 2020 |
Title | LAMMPS CG-DNA package |
Description | A simulation package for coarse-grained simulation of DNA and RNA |
Type Of Technology | Software |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | The LAMMPS code is used by 1000s of researchers. The CG-DNA package is used in dozens of groups worldwide. |
URL | https://www.lammps.org |
Title | LAMMPS USER-CGDNA package |
Description | LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. The oxDNA model for coarse-grained modelling of DNA is now also available as LAMMPS USER-package. |
Type Of Technology | Software |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | The oxDNA model is now more easily accessible to a global user community of the LAMMPS code. |
URL | http://lammps.sandia.gov |
Title | Ludwig Soft Matter Simulation Software |
Description | The lattice-Boltzmann simulation package for soft matter and complex fluid 'Ludwig' is developed in a longterm collaboration between the School of Physics, University of Edinburgh and the Edinburgh Parallel Computing Centre. |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | New improvements in the electrokinetic and liquid-crystalline functionalities have been implemented and were released. The user base has been extended and includes now new researchers at the University of Cambridge and Oxford, who will be using Ludwig for their research. |
URL | http://ludwig.epcc.ed.ac.uk |
Title | ohenrich/cgdna: oxDNA2 |
Description | The LAMMPS-based oxDNA (v1.0) has been extended to the oxDNA2 model, which features improved structure and sequence-dependent hydrogen-bonding and stacking interactions. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | We notice an increased interest in the LAMMPS implementation of the oxDNA model. |
Title | ohenrich/cgdna: oxRNA2 |
Description | The LAMMPS-based oxDNA (v1.0) and oxDNA2 (v2.0) implementations have been extended to include now the oxRNA2 coarse-grained model for RNA. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | We notice an increased interest in the LAMMPS implementation of the oxDNA model. |
Title | tacoxDNA |
Description | We added additional functionality to tacoxDNA, the suite of tools and converters which offers a simple interface for converting various common formats of DNA structures and for setting up molecular dynamics simulations. tacoxDNA allows users to produce complex DNA geometries with or without supercoiling by simply providing an XYZ coordinate file of the DNA centre-line or by using blueprints generated with the cadnano, CanDo, Tiamat and vHelix tools. It can also assist in the conversion to and from all-atom or oxDNA representations. The current version of tacoxDNA focusses on oxDNA, but its source code been designed so that users can straightforwardly expand it to support other formats and add more functionalities. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | Improved and more detailed visualisation and substantially improved data manipulation capabilities for trajectories in LAMMPS format. |
Description | Higgs Centre for Theoretical Physics Workshop 'DNA Supercoiling', Santadi, Sardinia, Italy |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | 25 researchers attended this international workshop on DNA supercoiling, statistical physics, theoretical models and experiments. |
Year(s) Of Engagement Activity | 2023 |
Description | SIAM Conference on Mathematical Aspects of Materials Science 2021 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Over 100 scientists attended this talk, which sparked questions and discussions. |
Year(s) Of Engagement Activity | 2021 |
Description | oxDNA User and Developer Workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The first oxDNA User and Developer Workshop took place in September 2019 in Oxford. The purpose of this activity was to bring the global community of users and developers together, coordinate development activities and decide on the next steps. |
Year(s) Of Engagement Activity | 2019 |