Related papers: Thermodynamic Binding Networks
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
Physics-informed neural network architectures have emerged as a powerful tool for developing flexible PDE solvers which easily assimilate data, but face challenges related to the PDE discretization underpinning them. By instead adapting a…
The thermodynamic binding networks (TBN) model is a tool for studying engineered molecular systems. The TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition,…
The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which…
Development of thermodynamic induction up to second order gives a dynamical bifurcation for thermodynamic variables and allows for the prediction and detailed explanation of nonequilibrium phase transitions with associated spontaneous…
In systems with detailed balance, the stationary distribution and the equilibrium distribution are identical, creating a clear connection between energetic and entropic quantities. Many driven systems violate detailed balance and still pose…
We study nonequilibrium thermodynamics in a fermionic resonant level model with arbitrary coupling strength to a fermionic bath, taking the wide-band limit. In contrast to previous theories, we consider a system where both the level energy…
In the real world, one almost never knows the parameters of a thermodynamic process to infinite precision. Reflecting this, here we investigate how to extend stochastic thermodynamics to systems with uncertain parameters, including…
We examine stochastic processes that are used to model nonequilibrium processes (e.g, pulling RNA or dragging colloids) and so deliberately violate detailed balance. We argue that by combining an information-theoretic measure of…
An information theoretic approach inspired by quantum statistical mechanics was recently proposed as a means to optimize network models and to assess their likelihood against synthetic and real-world networks. Importantly, this method does…
In the paradigm of thermodynamic computing, instead of behaving deterministically, hardware undergoes a stochastic process in order to sample from a distribution of interest. While it has been hypothesized that thermodynamic computers may…
We prove that the transport of any differentiable scalar observable in $d$-dimensional non-equilibrium systems is bounded from above by the total entropy production scaled by the amount the observation "stretches" microscopic coordinates.…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
We present the design for a thermodynamic computer that can perform arbitrary nonlinear calculations in or out of equilibrium. Simple thermodynamic circuits, fluctuating degrees of freedom in contact with a thermal bath and confined by a…
The problem of the insensitivity of the macroscopic behavior of any thermodynamical system to partitioning generates a bias between the reproducibility of its macroscopic behavior viewed as the simplest form of causality and its long-term…
Biological and engineered systems operate by coupling function to the transfer of heat and/or particles down a thermal or chemical gradient. In idealized \textit{deterministically} driven systems, thermodynamic control can be exerted…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
A communication theory for a transmitter broadcasting to many receivers is presented. In this case energetic considerations cannot be neglected as in Shannon theory. It is shown that, when energy is assigned to the information bit,…