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Benjamin Qureshi

Publications and source records attributed to Benjamin Qureshi.

2 recordsLinked to original sources

Recurrent neural chemical reaction networks that approximate arbitrary dynamics

Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such rich dynamics is a challenging problem central to the fields of synthetic biology and molecular nanotechnology. In this paper, we address this problem by putting forward a molecular version of a recurrent artificial neural network, which we call recurrent neural chemical reaction network (RNCRN). The RNCRN uses a modular architecture - a network of chemical neurons - to approximate arbitrary dynamics. We first prove that with sufficiently many chemical neurons and suitably fast reactions, the RNCRN can be systematically trained to achieve any dynamics. RNCRNs with relatively small number of chemical neurons and a moderate range of reaction rates are then trained to display a variety of biologically-important dynamical features. We also demonstrate that such RNCRNs are experimentally implementable with DNA-strand-displacement technologies.

q-bio.MN

Thermodynamic limits on general far-from-equilibrium molecular templating networks

Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property of the network, regardless of complexity. Surprisingly, putative systems operating at this bound do not have a high flux around the network. Instead, they have low entropy production, with each product in a ``pseudo-equilibrium'' determined by a single pathway. These pseudo-equilibrium limits constrain information transmission for the overall network, even if individual templates are arbitrarily specific.

physics.bio-ph