Research

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Equal and Opposite reaction

Visit our blog to find out our take on the latest developments in the field.

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Publications

Below is a summary of our work. A full list of Tom's publications can be found on google scholar.

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Open access links

Many of the links below are to journals which require a subscription. Most of our work can be accessed via Imperial's open access repository, after a short embargo period.

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Topics

Recent Highlights

16/03/2023 A universal method for analyzing copolymer growth

[10:02 AM] Qureshi, Benjamin

Copolymers are polymers consisting of multiple types of monomers like DNA or RNA with different nucleotides or proteins with amino acids. They are the way by which biology stores information and creates its machinery. Copolymers may be created either with or without the use of a template which is another molecule which biases the production of a single sequence of monomers. For example, messenger RNA templates the production of proteins. The process by which monomers are added into a growing copolymer chain may, in general, be complicated and multi-step, for example in the case of kinetic proofreading where fuel is burned to decrease the chances of errors. In this paper, we introduce a new method for analysing these copolymerisation processes where monomers are added or removed from a growing chain via complicated, multi-step mechanisms. From this we are able to extract not only statistical information about the distribution of sequences of monomers produced, but also kinetic information about how long these processes take and how much work is done.  

 

04/02/2022 Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers

Synthetic RNA systems offer unique advantages such as faster response, increased specificity, and programmability compared to conventional protein-based networks. In this work, we demonstrate an in vitro RNA-based toggle switch using RNA aptamers capable of inhibiting the transcriptional activity of T7 or SP6 RNA polymerases. The activities of both polymerases are monitored simultaneously by using Broccoli and Malachite green light-up aptamer systems.  

In our toggle switch, a T7 promoter drives the expression of SP6 inhibitory aptamers, and an SP6 promoter expresses T7 inhibitory aptamers. We show that the two distinct states originating from the mutual inhibition of aptamers can be toggled by adding DNA sequences to sequester the RNA inhibitory aptamers.  We assessed our RNA-based toggle switch in degrading conditions by introducing controlled degradation of RNAs using a mix of RNases. Our results demonstrate that the RNA-based toggle switch could be used as a control element for nucleic acid networks in synthetic biology applications. 

07/11/2021 Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the superficially similar process of self-assembly, however, the development of synthetic systems that implement templated copying of copolymers has been challenging. The main difficulty has been overcoming product inhibition, or the tendency of products to adhere strongly to their templates -- an effect that gets exponentially worse with template length. We first demonstrate product inhibition in a minimal model of template binding and polymerisation, then ask how this model might be modified to give cyclic production of polymer copies of the right length and sequence in an autonomous and chemically-driven context. We find that a relatively simple extension is sufficient to generate far longer polymer products that form on and then separate from, the template. In this approach, some of the free energy of polymerisation is diverted into disrupting copy-template bonds behind the leading edge of the copy. By additionally weakening the final copy-template bond at the end of the template, we are able to demonstrate that reliable copying with a high yield of full-length, sequence-matched products is possible over large ranges of parameter space, opening the way to the engineering of synthetic copying systems.

17/06/2021 A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model’s fundamental properties. We outline how simulation results can be interpreted in terms of—and feed into our understanding of—less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.

01/05/2021, Integral feedback in synthetic biology: Negative-equilibrium catastrophe submitted

A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner. To address the fact that detailed knowledge about intracellular networks is unavailable, integral-feedback controllers (IFCs) have been put forward for controlling molecular abundances. These controllers can maintain accuracy in spite of the uncertainties in the controlled networks. However, this desirable feature is achieved only if stability is also maintained. In this paper, we show that molecular IFCs can suffer from a hazardous instability called negative-equilibrium catastrophe (NEC), whereby all nonnegative equilibria vanish under the action of the controllers, and some of the molecular abundances blow up. We show that unimolecular IFCs do not exist due to a NEC. We then derive a family of bimolecular IFCs that are safeguarded against NECs when uncertain unimolecular networks, with any number of molecular species, are controlled. However, when IFCs are applied on uncertain bimolecular (and hence most intracellular) networks, we show that preventing NECs generally becomes an intractable problem as the number of interacting molecular species increases.

05/02/2021, What would it take to build a thermodynamically reversible Universal Turing machine? Computational and thermodynamic constraints in a molecular design submitted

We outline the construction of a molecular system that could, in principle, implement a thermodynamically reversible Universal Turing Machine (UTM). By proposing a concrete-albeit idealised-design and operational protocol, we reveal fundamental challenges that arise when attempting to implement arbitrary computations reversibly. Firstly, the requirements of thermodynamic reversibility inevitably lead to an intricate design. Secondly, thermodynamically reversible UTMs, unlike simpler devices, must also be logically reversible. Finally, implementing multiple distinct computations in parallel is necessary to take the cost of external control per computation to zero, but this approach is complicated the distinct halting times of different computations.

Functional molecular systems

 

Push-pull
A characteristic enzymatic signalling motif in which readouts (orange) are activated by receptors (Y-shaped molecules) bound to ligands (blue). This process not only passes on a signal, but allows time integration since multiple readouts can store stable copies of receptor states over time.

 

Biochemical networks within cells achieve remarkable functionality, including sensing, signalling, information-processing and replication. We aim to understand the fundamental physical principles that set the scope of this behaviour, allowing development of engineering principles for artificial analogs of these systems.

Since these systems of interest typically involve small numbers of molecules, randomness plays an important role. This work often touches on the deep connections between two bodies of work that deal explicitly with randomness: information theory, which describes the role of randomness in communication, and statistical mechanics, through which randomness is related to thermodynamics.

Recently, we've started to translate our basic understanding into the engineering of synthetic, nucleic acid-based analogs of these natural systems within our own lab here at Imperial. To get a taste, check out Javi's talk at FNANO2020, or a simplified discussion of his overall project. 

Relevant Publications

  1. Qureshi, B., Juritz, J., Poulton, J. M., Beersing-Vasquez, A., & Ouldridge, T. E. (2023). A universal method for analyzing copolymer growth. The Journal of Chemical Physics, 158(10), 104906.
  2. Catala AC, Ouldridge TE, Stan GBV, Bae W, 2022, "Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers", ACS synthetic biology, 11(2), 562-569.
  3. Juritz J, Poulton JM, Ouldridge TE, 2021, "Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions", The Journal of Chemical Physics, 156(7), 074103.
  4. Plesa T, Dack A, Ouldridge TE, "Integral feedback in synthetic biology: Negative-equilibrium catastrophe", submitted.
  5. Bae W, Stan GBV, Ouldridge TE, 2021, "In situ generation of RNA complexes for synthetic molecular strand displacement circuits in autonomous systems", Nano Lett. , 21, 1, 265–271
  6. Cabello-Garcia J, Bae W, Stan GBV, Ouldridge TE, 2021, "Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions", ACS Nano, 15, 2, 3272–3283.
  7. Poulton JM, Ouldridge TE, 2021, "Edge-effects dominate copying thermodynamics for finite-length molecular oligomers", New J. Phys. 23 063061.
  8. Lankinen A, Mullor Ruiz I, Ouldridge TE, "Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts", submitted. 
  9. Plesa T, Stan G-BV, Ouldridge TE, Bae W, 2021, "Quasi-robust control of biochemical reaction networks via stochastic morphing", J. R. Soc. Interface.1820200985.
  10. Deshpande A, Ouldridge TE, 2020, "Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration". Biological Cybernetics volume 114, 653–668
  11. Brittain RA, Jones NS, Ouldridge TE, 2019, Biochemical Szilard engines for memory-limited inference, New J. Phys. 21,063022.
  12. Poulton J, ten Wolde PR and Ouldridge TE, 2019, Non-equilibrium correlations in minimal dynamical models of polymer copying, PNAS: 116,1946-1951.
  13. Ouldridge TE, Brittain RA, ten Wolde PR, 2018, The power of being explicit: demystifying work, heat, and free energy in the physics of computation, in "The Energetics of Computing in Life and Machines", SFI Press.
  14. Deshpande A, Ouldridge  TE, 2017, High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits, Engineering Biology: 1,86-99.
  15. Poole W, Ortiz-Muñoz A, Behera A, Jones NS,  Ouldridge  TE, Winfree E, Gopalkrishnan M, 2017, Chemical Boltzmann Machines, In DNA Computing and Molecular Programming. DNA 2017. Lecture Notes in Computer Science: 10467,210-231.
  16. Brittain RA, Jones NS, Ouldridge TE, 2017, What we learn from the learning rate, J. Stat. Mech.: 063592.
  17. Ouldridge TE, 2017, The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics, Nat. Comput.: in press.
  18. Ouldridge TE, ten Wolde PR, 2017, Fundamental costs in the production and destruction of persistent polymer copies, Phys. Rev. Lett.: 118,158103.
  19. Ouldridge TE, Govern CC, ten Wolde PR, 2017, Thermodynamics of computational copying in biochemical system, Phys. Rev. X: 7,021004.
  20. McGrath T, Jones NS, ten Wolde PR, Ouldridge TE, 2017, Biochemical machines for the interconversion of mutual information and work, Phys. Rev. Lett.: 118,028101.
  21. ten Wolde PR, Becker NB, Ouldridge TE, Mugler A, 2015, Fundamental Limits to Cellular Sensing, J. Stat. Phys.: 162,1395-1424.
  22. Ouldridge TE, ten Wolde PR, 2014, The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway, Biophysical Journal: 107,2425-2435.

Coarse-grained modelling of DNA

 

disp fig

The elegant selectivity of Watson-Crick base-pairing makes DNA an extremely useful tool for the construction of nanoscale objects and machines. Stable structures and mechanical cycles can be programmed into a system of single strands by careful choice of the sequences of bases. I'm particularly interested in using nucleic acids to design artificial analogs of complex cellular systems, to enable careful exploration of the design principles and engineering possibilities.

Despite the experimental successes, there is no clear theoretical description of the processes involved. We have developed a nucleotide-level coarse grained model of DNA, oxDNA, which is detailed enough to capture the essential physics of assembly processes, yet simple enough to be applicable over long time scales. Code, user guides and examples for simulating the model can be downloaded from this site.

The oxDNA model was developed in the Doye / Louis groups in Oxford. It has since been applied in collaboration with the Turberfield group in Oxford, the Winfree group in Caltech and the Nir group at the Ben-Gurion University of Negev, as well as being used independently by other researchers.

Even with oxDNA, it is still not practical to simulate the formation of very large structures. A collaboration with the Turberfield and Kwiatkowska groups in Oxford has led to a less detailed model that can describe the formation of DNA origami structures.

Relevant Publications

  1. Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Sulc P, 2021, "A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results", Frontiers in molecular biosciences, 8, 551.
  2. Irmisch P, Ouldridge TE, Seidel R, 2020, "Modelling DNA-strand displacement reactions in the presence of base-pair mismatches", J. Am. Chem. Soc., 142, 26, 11451–11463
  3. Haley NEC, Ouldridge TE, Mullor Ruiz I, Geraldini A, Louis AA, Bath J and Turberfield AA, 2020, Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement, Nat. Comms. 11:2562.
  4. Lankinen A, Mullor Ruiz I, Ouldridge TE, "Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts", submitted. 
  5. Fonseca P, Romano F, Schreck JS, Ouldridge TE, Doye JPK and Louis AA, 2018, Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly, J. Chem. Phys. 148:134910. 
  6. Khara DC, Schreck JS, Tomov TE, Berger Y, Ouldridge TE, Doye JPK and Nir E, 2018, DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size, Nucl. Acids Res. 46:1553-1561.
  7. Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, and Doye JPK, 2016, Direct Simulation of the Self-Assembly of a Small DNA Origami, ACS Nano: 10,1724-1737.
  8. Dunn KE, Dannenberg F, Ouldridge TE, Kwiatkowska M, Turberfield AJ, Bath J, 2015, Guiding the folding pathway of DNA origami, Nature: 525,82-86.
  9. Dannenberg F, Dunn KE, Bath J, Kwiatkowska M, Turberfield AJ, Ouldridge TE, 2015, Modelling DNA Origami Self-Assembly at the Domain Level, J. Chem. Phys.: 143,165102.
  10. Snodin BEK, Randisi F, Mosayebi M, Sulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPK, 2015, Introducing improved structural properties and salt dependence into a coarse-grained model of DNA, J. Chem. Phys.: 142,234901.
  11. Schreck JS, Ouldridge TE, Romano F, Sulc P, Shaw L, Louis AA, Doye JPK, 2015, DNA hairpins primarily promote duplex melting rather than inhibiting hybridization, Nucleic Acids Research: 43,6181-6190.
  12. Mosayebi M, Louis AA, Doye JPK, Ouldridge TE, 2015, Force-induced rupture of a DNA duplex, ACS Nano: 9,11993-12003.
  13. Machinek RR, Ouldridge TE, Haley NE, Bath J, Turberfield AJ, 2014, Programmable energy landscapes for kinetic control of DNA strand displacement, Nature Communications: 5,5324.
  14. Doye JPK, Ouldridge TE, Louis AA, Romano F, Sulc P, Matek C, Snodin BEK, Rovigatti L, Schreck JS, Harrison RM, Smith WPJ, 2013, Coarse-graining DNA for simulations of DNA nanotechnology, Physical Chemistry Chemical Physics: 15,20395-20414.
  15. Srinivas N, Ouldridge TE, Sulc P, Schaeffer JM, Yurke B, Louis AA, Doye JPK, Winfree E, 2013, On the biophysics and kinetics of toehold-mediated DNA strand displacement, Nucleic Acids Research: 41,10641-10658.
  16. Ouldridge TE, Sulc P, Romano F, Doye JPK, Louis AA, 2013, DNA hybridization kinetics: Zippering, internal displacement and sequence dependence, Nucleic Acids Research: 41,8886-8895.
  17. Ouldridge TE, Hoare RL, Louis AA, Doye JPK, Bath J, Turberfield AJ, 2013, Optimizing DNA nanotechnology through coarse-grained modeling: A two-footed DNA walker, ACS Nano: 7,2479-2490.
  18. Sulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JPK, Louis AA, 2012, Sequence-dependent thermodynamics of a coarse-grained DNA model, Journal of Chemical Physics: 137,135101.
  19. Ouldridge TE, Louis AA, Doye JPK, 2011, Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model, Journal of Chemical Physics: 134,085101.
  20. Ouldridge TE, Louis AA, Doye JPK, 2010, DNA nanotweezers studied with a coarse-grained model of DNA, Physical Review Letters: 104,178101.

Thermodynamics of small systems

Thermodynamics, the science of heat and energy transfer, emerged as a field in the 19th century, motivated by the need to describe the engines that powered the industrial revolution. One of the challenges of modern science is to adapt and extend the theory to describe microscopic systems in which fluctuations play a key role. Biological and biologically-inspired systems are a key arena for these new ideas, due both to the need to understand natural molecular analogues of the engines and processes that we are familiar with at much larger length scales, and the possibility of developing artificial devices ourselves.

Not only does thermodynamics provide understanding of biological systems, but the study of real biophysical devices in turn provides us with a deeper understanding of the thermodynamic principles at play. In particular, the natural diffusive behaviour of biomolecules allows us to study complex systems that do not require external manipulation to function.

Relevant Publications

  1. Ouldridge, T. E., & Wolpert, D. H. (2022). Thermodynamics of deterministic finite automata operating locally and periodically. arXiv preprint arXiv:2208.06895. 
  2. Juritz J, Poulton JM, Ouldridge TE, 2021 "Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions", submitted
  3. Brittain RA, Jones NS, Ouldridge TE, "What would it take to build a thermodynamically reversible Universal Turing machine? Computational and thermodynamic constraints in a molecular design", submitted.
  4. Poulton JM, Ouldridge TE, 2021, "Edge-effects dominate copying thermodynamics for finite-length molecular oligomers", New J. Phys. 23 063061.
  5. Ouldridge TE, 2020, A biochemical device To demystify a century-old thermodynamics puzzle from theoretical physics, Reseach Outreach: 112. 
  6. Brittain RA, Jones NS, Ouldridge TE, 2019, Biochemical Szilard engines for memory-limited inference, in press at New. J. Phys.
  7. Ouldridge TW, Brittain RA, ten Wolde PR, 2019, The power of being explicit: demystifying work, heat, and free energy in the physics of computation, in "The Energetics of Computing in Life and Machines", SFI Press.
  8. Stopnitzky E, Still S, Ouldridge TE and Altenberg L, 2019,  Physical Limitations of Work Extraction from Temporal Correlations, Phys. Rev. E: 99,042115. 
  9. Poulton J, ten Wolde PR and Ouldridge TE, 2019, Non-equilibrium correlations in minimal dynamical models of polymer copying, PNAS: 116,1946-1951.
  10. Deshpande A, Ouldridge  TE, 2017, High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits, Engineering Biology: 1,86-99.
  11. Deshpande A, Gopalkrishnan M, Ouldridge TE, Jones NS, 2017,  Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability, Proc. Roy. Soc. A.: 473,20170117.
  12. Brittain RA, Jones NS, Ouldridge TE, 2017, What we learn from the learning rate, J. Stat. Mech.: 063592.
  13. Ouldridge TE, 2017, The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics, Nat. Comput.: in press.
  14. Ouldridge TE, ten Wolde PR, 2017, Fundamental costs in the production and destruction of persistent polymer copies, Phys. Rev. Lett.: 118,158103.
  15. Ouldridge TE, Govern CC, ten Wolde PR, 2017, Thermodynamics of computational copying in biochemical system, Phys. Rev. X: 7,021004.
  16. McGrath T, Jones NS, ten Wolde PR, Ouldridge TE, 2017, Biochemical machines for the interconversion of mutual information and work, Phys. Rev. Lett.: 118,028101.

Simulation tools and algorithms

Our work often involves systems that are too complex to be treated analytically. This means that simulations are a key tool in our research, and we are interested in simulation techniques and analysis tools for systems involving biomolecular reactions.

In this work we collaborate with the Doye / Louis groups in Oxford, the biochemical networks group of Pieter Rein ten Wolde in Amsterdam, Michael Tretyakov in Nottingham and Ruslan Davidchack in Leicester, and Oliver Henrich in Strathclyde.

Relevant Publications

  1. Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Sulc P, 2021, "A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results", Frontiers in molecular biosciences, 8, 551.
  2. Henrich O, Yair AGF, Curk T, Ouldridge TE, 2018, Coarse-grained simulation of DNA using LAMMPS, Eur. Phys. J. E., 41: 57.
  3. Davidchack RL, Ouldridge TE, Tretyakov MV, 2017, Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions, J. Chem. Phys., 147:224103.
  4. Vijaykumar A, Ouldridge TE, ten Wolde PR, Bolhuis PG 2017, Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics,  Journal of Chemical Physics: 146,114106.
  5. Davidchack RL, Ouldridge TE, Tretyakov MV, 2015, New Langevin and Gradient Thermostats for Rigid Body Dynamics, Journal of Chemical Physics: 142,144114.
  6. Ouldridge TE, 2012, Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble, Journal of Chemical Physics: 137,144105.
  7. Ouldridge TE, Louis AA, Doye JPK, 2010, Extracting bulk properties of self-assembling systems from small simulations, Journal of Physics: Condensed Matter: 22,104102.

Biomolecular Engineering

 

 

HMSD
Data from Javi's paper on handhold-mediated strand displacement, showing that handholds reliably accelerate the rate of strand displacement

We've recently acquired our own (small) lab within the synthetic biology space at Imperial. We're using this lab to actually put our theoretical ideas into practice, engineering functional molecular systems from nucleic acids. These systems are both useful test-beds for our theory and engineering platforms for synthetic biology.

Our work currently focusses on engineering non-equilibrium information processing systems, analogs of the signalling and transcription/translation machinery in cells.  To get a taste, check out Javi's talk at FNANO2020, or a simplified discussion of his overall project. 

 

 

Relevant Publications

  1. Liu H, Hong F, Smith F, Goertz J, Ouldridge TE, Yan H, Sulc P, 2021, "Kinetics of RNA and RNA:DNA hybrid strand displacement", ACS Synth. Biol. , XXXX.
  2. Bae W, Stan GBV, Ouldridge TE, 2021, "In situ generation of RNA complexes for synthetic molecular strand displacement circuits in autonomous systems", Nano Lett. , 21, 1, 265–271
  3. Cabello-Garcia J, Bae W, Stan GBV, Ouldridge TE, 2021, "Handhold-mediated strand displacement: a nucleic acid-based mechanism for generating far-from-equilibrium assemblies through templated reactions", ACS Nano, 15, 2, 3272–3283.