A schematic model for molecular affinity and binding with Ising variables

Thalmann, Fabrice

doi:10.1140/epje/i2010-10600-9

Cited by 1 publication

(1 citation statement)

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“…The examples of such optimal design problems in chemistry and physics include the understanding of adaptiveness or binding affinity in the molecular recognition process within the lock-and-key paradigm 7 , 8 , which turns out to be very sensitive to molecular parameters 9 ; the search for polymer sequence design in protein folding 10 , the interaction potentials for optimal self-assembly 11 , the search for dynamic exchange of components in response to environmental conditions 12 , the prediction of a sequence of cell-penetrating peptides 13 , inverse design problems in nanophotonics 14 , 15 .…”

Section: Introductionmentioning

confidence: 99%

Efficient enumeration-selection computational strategy for adaptive chemistry

Guo

Werner

Baulin

2022

Sci Rep

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Design problems of finding efficient patterns, adaptation of complex molecules to external environments, affinity of molecules to specific targets, dynamic adaptive behavior of chemical systems, reconstruction of 3D structures from diffraction data are examples of difficult to solve optimal design or inverse search problems. Nature inspires evolution strategies to solve design problems that are based on selection of successful adaptations and heritable traits over generations. To exploit this strategy in the creation of new materials, a concept of adaptive chemistry was proposed to provide a route for synthesis of self-adapting molecules that can fit to their environment. We propose a computational method of an efficient exhaustive search exploiting massive parallelization on modern GPUs, which finds a solution for an inverse problem by solving repetitively a direct problem in the mean field approximation. One example is the search for a composition of a copolymer that allows the polymer to translocate through a lipid membrane at a minimal time. Another example is a search of a copolymer sequence that maximizes the polymer load in the micelle defined by the radial core-shell potentials. The length and the composition of the sequence are adjusted to fit into the restricted environment. Hydrogen bonding is another pathway of adaptation to the environment through reversible links. A linear polymer that interacts with water through hydrogen bonds adjusts the position of hydrogen bonds along the chain as a function of the concentration field around monomers. In the last example, branching of the molecules is adjusted to external fields, providing molecules with annealed topology, that can be flexibly changed by changing external conditions. The method can be generalized and applied to a broad spectrum of design problems in chemistry and physics, where adaptive behavior in multi-parameter space in response to environmental conditions lead to non-trivial patterns or molecule architectures and compositions. It can further be combined with machine learning or other optimization techniques to explore more efficiently the parameter space.

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Section: Introductionmentioning

confidence: 99%