Related papers: Thermodynamic Binding Networks
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
A theory for thermodynamic induction (TI) under isothermal conditions is presented. This includes a treatment of the Helmholtz free energy budget available for a gate variable to utilize towards aiding another variable's approach towards…
We consider viscous, heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, we derive a closed system of…
Surface-active agents (surfactants) release potential energy as they migrate from one of two adjacent fluids onto their fluid-fluid interface, a process that profoundly impacts the system's energy and entropy householding. The continuum…
We introduce thermodynamic networks, a general framework for autonomous, physics-based computation using non-equilibrium steady states. These networks are modeled as a collection of finite-size reservoirs that exchange conserved…
A consistent description of simultaneous heat and particle transport, including cross effects, and the associated entropy balance is given in the framework of a deterministic dynamical system. This is achieved by a multibaker map where,…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
The 2nd law of thermodynamics yields an irreversible increase in entropy until thermal equilibrium is achieved. This irreversible increase is often assumed to require large and complex systems to emerge from the reversible microscopic laws…
The thermodynamics of quantum systems coupled to periodically modulated heat baths and work reservoirs is developed. By identifying affinities and fluxes, the first and second law are formulated consistently. In the linear response regime,…
The concept of entropy in nonequilibrium macroscopic systems is investigated in the light of an extended equation of motion for the density matrix obtained in a previous study. It is found that a time-dependent information entropy can be…
Simulations are performed of a small quantum system interacting with a quantum environment. The system consists of various initial states of two harmonic oscillators coupled to give normal modes. The environment is "designed" by its level…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
We present a consistent thermodynamic theory for the resonant level model in the wide band limit, whose level energy is driven slowly by an external force. The problem of defining 'system' and 'bath' in the strong coupling regime is…
This work presents a general unifying theoretical framework for quantum non-equilibrium systems. It is based on a re-statement of the dynamical problem as one of inferring the distribution of collision events that move a system toward…
Equilibrium statistical mechanics provides a robust framework for characterizing phase transitions in systems whose microsopic dynamics are time-reversible. Efforts to develop and validate theoretical frameworks for time-irreversible,…
The emergence of irreversibility in physical processes, despite the fundamentally reversible nature of quantum mechanics, remains an open question in physics. This thesis explores the intricate relationship between quantum mechanics and…
In this study, we advance the understanding of non-equilibrium systems by deriving thermodynamic relations for a heat engine operating under an exponentially decreasing temperature profile. Such thermal configurations closely mimic…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
We introduce a constructive framework for assigning thermodynamic structure to an arbitrary data system from its measured microstates. Starting from an empirical distribution over configurations, we first infer a data-driven energy function…