Related papers: Markov Blanket Density and Free Energy Minimizatio…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
In this work, a lower bound for the ground state energy of the Falicov-Kimball model for intermediate densities is derived. The explicit derivation is important in the proof of the conjecture of segregation of the two kinds of fermions in…
We derive the Planck law from a classical variational principle over probability densities, without invoking quantum states, quantized oscillator energies, or ensemble averages. We construct a generalized free energy functional involving…
The Free-Energy Principle (FEP) [1-3] has been adopted in a variety of ambitious proposals that aim to characterize all adaptive, sentient, and cognitive systems within a unifying framework. Judging by the amount of attention it has…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
An overarching action principle, the principle of minimal free action, exists for ergodic Markov chain dynamics. Using this principle and the Detailed Fluctuation Theorem, we construct a dynamic ensemble theory for non-equilibrium steady…
Organisms are nonequilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy principle describes an…
The analysis of high-dimensional time series data has become increasingly important across a wide range of fields. Recently, a method for constructing the minimum information Markov kernel on finite state spaces was established. In this…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
Scale free dynamics are observed in a variety of physical and biological systems. These include neural activity in which evidence for scale freeness has been reported using a range of imaging modalities. Here, we derive the ways in which…
In a previous paper, a bound on the negative energy density seen by an arbitrary inertial observer was derived for the free massless, quantized scalar field in four-dimensional Minkowski spacetime. This constraint has the form of an…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
We present a detailed analysis of the universal relationship between grain boundary (GB) free energy and GB self-diffusion coefficient derived by Borisov et al. (1964). This relationship was expressed by a simple equation that was used in…
Two high-level "pictures" of probability theory have emerged: one that takes as central the notion of random variable, and one that focuses on distributions and probability channels (Markov kernels). While the channel-based picture has been…
A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
This thesis focuses on three fundamental aspects of biological systems; namely, entropy production, Bayesian mechanics, and the free-energy principle. The contributions are threefold: 1) We compute the entropy production for a greater class…
A family of fast sampling methods is introduced here for molecular simulations of systems having rugged free energy landscapes. The methods represent a generalization of a strategy consisting of adjusting a model for the free energy as a…
Information-theoretic principles for learning and acting have been proposed to solve particular classes of Markov Decision Problems. Mathematically, such approaches are governed by a variational free energy principle and allow solving MDP…