Practical, useful computations are instantiated via physical processes. Information must be stored and updated within a system's configurations, whose energetics determine a computation's cost. To describe thermodynamic and biological information processing, a growing body of results embraces rate equations as the underlying mechanics of computation. Strictly applying these continuous-time stochastic Markov dynamics, however, precludes a universe of natural computing. Within this framework, operations as simple as a NOT gate (flipping a bit) and swapping two bits, and swapping bits are inaccessible. We show that expanding the toolset to continuous-time hidden Markov dynamics substantially removes the constraints, by allowing information to be stored in a system's latent states. We demonstrate this by simulating computations that are impossible to implement without hidden states. We design and analyze a thermodynamically costless bit flip, providing a counterexample to rate-equation modeling. We generalize this to a costless Fredkin gate - a key operation in reversible computing that is Turing complete (computation universal). Going beyond rate-equation dynamics is not only possible but also necessary if stochastic thermodynamics is to become part of the paradigm for physical information processing.

Modern digital electronics support remarkably reliable computing, especially given the challenge of controlling nanoscale logical components that interact in fluctuating environments. However, we demonstrate that the high-reliability limit is subject to a fundamental error-energy-efficiency tradeoff that arises from time-symmetric control: Requiring a low probability of error causes energy consumption to diverge as the logarithm of the inverse error rate for nonreciprocal logical transitions. The reciprocity (self-invertibility) of a computation is a stricter condition for thermodynamic efficiency than logical reversibility (invertibility), the latter being the root of Landauer's work bound on erasing information. Beyond engineered computation, the results identify a generic error-dissipation tradeoff in steady-state transformations of genetic information carried out by biological organisms. The lesson is that computational dissipation under time-symmetric control cannot reach, and is often far above, the Landauer limit. In this way, time-asymmetry becomes a design principle for thermodynamically efficient computing.

Nonequilibrium information thermodynamics determines the minimum energy dissipation to reliably erase memory under time-symmetric control protocols. We demonstrate that its bounds are tight and so show that the costs overwhelm those implied by Landauer’s energy bound on information erasure. Moreover, in the limit of perfect computation, the costs diverge. The conclusion is that time-asymmetric protocols should be developed for efficient, accurate thermodynamic computing. And, that Landauer’s Stack—the full suite of theoretically-predicted thermodynamic costs—is ready for experimental test and calibration.

All computation is physically embedded. Reflecting this, a growing body of results embraces rate equations as the underlying mechanics of thermodynamic computation and biological information processing. Strictly applying the implied continuous-time Markov chains, however, excludes a universe of natural computing. We show that expanding the toolset to continuous-time hidden Markov chains substantially removes the constraints. The general point is made concrete by our analyzing two eminently-useful computations that are impossible to describe with a set of rate equations over the memory states. We design and analyze a thermodynamically-costless bit flip, providing a first counterexample to rate-equation modeling. We generalize this to a costless Fredkin gate---a key operation in reversible computing that is computation universal. Going beyond rate-equation dynamics is not only possible, but necessary if stochastic thermodynamics is to become part of the paradigm for physical information processing.