arXiv subjects

Charles D. Kocher

Publications and source records attributed to Charles D. Kocher.

3 recordsLinked to original sources

arXiv2026

Nonequilibrium Theory for Adaptive Systems in Varying Environments

Biological organisms are adaptive, able to function in unpredictably changing environments. Drawing on recent nonequilibrium physics, we show that in adaptation, fitness has two components parameterized by observable coordinates: a static Generalism component characterized by state distributions, and a dynamic Tracking component sustained by nonequilibrium fluxes. Our findings: (1) General Theory: We prove that tracking gain scales strictly with environmental variability and switching time-scales; near-static or fast-switching environments are not worth tracking. (2) Optimal Strategies: We explain optimal bet-hedging and phenotypic memory as the interplay between these components. (3) Control: We demonstrate, with an example, how to suppress pathogens by independently attacking their Generalism robustness (via environmental time fractions) and Tracking capabilities (via environmental switching speed). This work provides a physical framework for understanding and controlling adaptivity.

cond-mat.stat-mech↗

arXiv2023

The prebiotic emergence of biological evolution

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyze the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.

q-bio.PE↗

arXiv2018

Simulating 0+1 Dimensional Quantum Gravity on Quantum Computers: Mini-Superspace Quantum Cosmology and the World Line Approach in Quantum Field Theory

Quantum computers are a promising candidate to radically expand computational science through increased computing power and more effective algorithms. In particular quantum computing could have a tremendous impact in the field of quantum cosmology. The goal of quantum cosmology is to describe the evolution of the Universe through the Wheeler-DeWitt equation or path integral methods without having to first formulate a full theory of quantum gravity. The quantum computer provides an advantage in this endeavor because it can perform path integrals in Lorentzian space and does not require constructing contour integrations in Euclidean gravity. Also quantum computers can provide advantages in systems with fermions which are difficult to analyze on classical computers. In this study, we first employed classical computational methods to analyze a Friedmann-Robertson-Walker mini-superspace with a scalar field and visualize the calculated wave function of the Universe for a variety of different values of the spatial curvature and cosmological constant. We them used IBM's Quantum Information Science Kit Python library and the variational quantum eigensolver to study the same systems on a quantum computer. The framework can also be extended to the world line approach to quantum field theory.

quant-ph↗