Search Results - "Louis, Ard. A"

Input–output maps are strongly biased towards simple outputs by Dingle, Kamaludin, Camargo, Chico Q., Louis, Ard A.

“…Many systems in nature can be described using discrete input–output maps. Without knowing details about a map, there may seem to be no a priori reason to…”
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The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima by Schaper, Steffen, Louis, Ard A

“…Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger…”
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On the biophysics and kinetics of toehold-mediated DNA strand displacement by Srinivas, Niranjan, Ouldridge, Thomas E, Sulc, Petr, Schaeffer, Joseph M, Yurke, Bernard, Louis, Ard A, Doye, Jonathan P K, Winfree, Erik

“…Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement…”
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Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model by Ouldridge, Thomas E, Louis, Ard A, Doye, Jonathan P K

“…We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study…”
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Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement by Haley, Natalie E. C., Ouldridge, Thomas E., Mullor Ruiz, Ismael, Geraldini, Alessandro, Louis, Ard A., Bath, Jonathan, Turberfield, Andrew J.

“…Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however,…”
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Sequence-dependent thermodynamics of a coarse-grained DNA model by Šulc, Petr, Romano, Flavio, Ouldridge, Thomas E, Rovigatti, Lorenzo, Doye, Jonathan P K, Louis, Ard A

“…We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101…”
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DNA hybridization kinetics: zippering, internal displacement and sequence dependence by Ouldridge, Thomas E, Sulc, Petr, Romano, Flavio, Doye, Jonathan P K, Louis, Ard A

“…Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such…”
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Measuring Internal Forces in Single-Stranded DNA: Application to a DNA Force Clamp by Engel, Megan C, Romano, Flavio, Louis, Ard. A, Doye, Jonathan P. K

“…We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The…”
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Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors by Mosayebi, Majid, Louis, Ard A, Doye, Jonathan P. K, Ouldridge, Thomas E

“…The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of…”
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Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs by Martin, Nora S, Camargo, Chico Q, Louis, Ard A

“…Biomorphs, Richard Dawkins's iconic model of morphological evolution, are traditionally used to demonstrate the power of natural selection to generate…”
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Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability by Greenbury, Sam F, Schaper, Steffen, Ahnert, Sebastian E, Louis, Ard A

“…Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such…”
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A nucleotide-level coarse-grained model of RNA by Šulc, Petr, Romano, Flavio, Ouldridge, Thomas E, Doye, Jonathan P K, Louis, Ard A

“…We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is…”
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Exploring Simplicity Bias in 1D Dynamical Systems by Dingle, Kamal, Alaskandarani, Mohammad, Hamzi, Boumediene, Louis, Ard A

“…Arguments inspired by algorithmic information theory predict an inverse relation between the probability and complexity of output patterns in a wide range of…”
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Coarse-graining DNA for simulations of DNA nanotechnology by Doye, Jonathan P K, Ouldridge, Thomas E, Louis, Ard A, Romano, Flavio, Šulc, Petr, Matek, Christian, Snodin, Benedict E K, Rovigatti, Lorenzo, Schreck, John S, Harrison, Ryan M, Smith, William P J

“…To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different…”
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Modelling Toehold-Mediated RNA Strand Displacement by Šulc, Petr, Ouldridge, Thomas E., Romano, Flavio, Doye, Jonathan P.K., Louis, Ard A.

“…We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand…”
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Controlling crystallization and its absence: proteins, colloids and patchy models by Doye, Jonathan P K, Louis, Ard A, Lin, I-Chun, Allen, Lucy R, Noya, Eva G, Wilber, Alex W, Kok, Hoong Chwan, Lyus, Rosie

“…The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids,…”
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Self-assembly of monodisperse clusters: Dependence on target geometry by Wilber, Alex W, Doye, Jonathan P K, Louis, Ard A

“…We apply a simple model system of patchy particles to study monodisperse self-assembly using the Platonic solids as target structures. We find marked…”
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Self-assembly and evolution of homomeric protein complexes by Villar, Gabriel, Wilber, Alex W, Williamson, Alex J, Thiara, Parvinder, Doye, Jonathan P K, Louis, Ard A, Jochum, Mara N, Lewis, Anna C F, Levy, Emmanuel D

“…We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow…”
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Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes by Dingle, Kamaludin, Ghaddar, Fatme, Šulc, Petr, Louis, Ard A

“…Abstract Morphospaces—representations of phenotypic characteristics—are often populated unevenly, leaving large parts unoccupied. Such patterns are typically…”
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Colloid-polymer mixtures in the protein limit by Bolhuis, Peter G, Meijer, Evert Jan, Louis, Ard A

“…We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit," where the polymer radius of gyration…”
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