Ouldridge, Thomas - Imperial College London - Department of Bioengineering

个人简介

I am just starting a Royal Society University Research Fellowship in the Bioengineering Department, where I will be building up a "Principles of Biomolecular Systems" group. I've previously been affiliated with Nick Jones' systems and signals group, the Doye / Louis biophysics groups in Oxford and the biochemical networks group of Pieter Rein ten Wolde in Amsterdam. My group probes the fundamental principles underlying complex biochemical systems through theoretical modelling, simulation and experiment. In particular, We focus on the interplay between the detailed biochemistry and the overall output of a process such as sensing, replication or self-assembly. We're inspired by natural systems, and aim to explore the possibilities of engineering artificial analogs.

近期论文

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McGrath T, Jones NS, Wolde PRT, Ouldridge TEet al., A biochemical machine for the interconversion of mutual information and work Ouldridge TE, Wolde PRT, Fundamental costs in the production and destruction of persistent polymer copies Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, Doye JPKet al., 2016, Direct Simulation of the Self-Assembly of a Small DNA Origami, ACS NANO, Vol: 10, Pages: 1724-1737, ISSN: 1936-0851 ten Wolde PR, Becker NB, Ouldridge TE, Mugler Aet al., 2016, Fundamental Limits to Cellular Sensing, JOURNAL OF STATISTICAL PHYSICS, Vol: 162, Pages: 1395-1424, ISSN: 0022-4715 Dannenberg F, Dunn KE, Bath J, Kwiatkowska M, Turberfield AJ, Ouldridge TEet al., 2015, Modelling DNA origami self-assembly at the domain level, JOURNAL OF CHEMICAL PHYSICS, Vol: 143, ISSN: 0021-9606 Davidchack RL, Ouldridge TE, Tretyakov MV, 2015, New Langevin and gradient thermostats for rigid body dynamics, JOURNAL OF CHEMICAL PHYSICS, Vol: 142, ISSN: 0021-9606 Dunn KE, Dannenberg F, Ouldridge TE, Kwiatkowska M, Turberfield AJ, Bath Jet al., 2015, Guiding the folding pathway of DNA origami., Nature, Vol: 525, Pages: 82-86 Harrison RM, Romano F, Ouldridge TE, Louis AA, Doye JPKet al., 2015, Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice" Harrison RM, Romano F, Ouldridge TE, Louis AA, Doye JPKet al., 2015, Coarse-grained modelling of strong DNA bending II: Cyclization Matek C, Ouldridge TE, Doye JP, Louis AAet al., 2015, Plectoneme tip bubbles: coupled denaturation and writhing in supercoiled DNA., Sci Rep, Vol: 5 Mosayebi M, Louis AA, Doye JPK, Ouldridge TEet al., 2015, Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors, ACS NANO, Vol: 9, Pages: 11993-12003, ISSN: 1936-0851 Ouldridge TE, Govern CC, Wolde PRT, 2015, The thermodynamics of computational copying in biochemical systems Schreck JS, Ouldridge TE, Romano F, Louis AA, Doye JPKet al., 2015, Characterizing the bending and flexibility induced by bulges in DNA duplexes, Journal of Chemical Physics, Vol: 142, ISSN: 1089-7690 Schreck JS, Ouldridge TE, Romano F, Sulc P, Shaw LP, Louis AA, Doye JPKet al., 2015, DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization, NUCLEIC ACIDS RESEARCH, Vol: 43, Pages: 6181-6190, ISSN: 0305-1048 Snodin BEK, Randisi F, Mosayebi M, Sulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPKet al., 2015, Introducing improved structural properties and salt dependence into a coarse-grained model of DNA, JOURNAL OF CHEMICAL PHYSICS, Vol: 142, ISSN: 0021-9606 Sulc P, Ouldridge TE, Romano F, Doye JPK, Louis AAet al., 2015, Modelling Toehold-Mediated RNA Strand Displacement, BIOPHYSICAL JOURNAL, Vol: 108, Pages: 1238-1247, ISSN: 0006-3495 Machinek RR, Ouldridge TE, Haley NE, Bath J, Turberfield AJet al., 2014, Programmable energy landscapes for kinetic control of DNA strand displacement., Nat Commun, Vol: 5 Mosayebi M, Romano F, Ouldridge TE, Louis AA, Doye JPet al., 2014, The role of loop stacking in the dynamics of DNA hairpin formation., J Phys Chem B, Vol: 118, Pages: 14326-14335 Ouldridge TE, 2014, DNA nanotechnology: understanding and optimisation through simulation, Molecular Physics, ISSN: 0026-8976 Ouldridge TE, Rein ten Wolde P, 2014, The robustness of proofreading to crowding-induced pseudo-processivity in the MAPK pathway., Biophys J, Vol: 107, Pages: 2425-2435