Related papers: Universal and accessible entropy estimation using …
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
In a recent Letter [1] a framework for estimating entropy was introduced and applied to one-dimensional and two-dimensional systems. In this Comment we show that the method is not well suited for estimating entropy in bidimensional systems…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
Language prediction is constrained by informational entropy intrinsic to language, such that there exists a limit to how accurate any language model can become and equivalently a lower bound to language compression. The most efficient…
Complex systems are characterised by a tight, nontrivial interplay of their constituents, which gives rise to a multi-scale spectrum of emergent properties. In this scenario, it is practically and conceptually difficult to identify those…
Algorithmic entropy can be seen as a special case of entropy as studied in statistical mechanics. This viewpoint allows us to apply many techniques developed for use in thermodynamics to the subject of algorithmic information theory. In…
We build a comprehensive methodology for the fast computation of entropy across both solid and liquid phases. The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is…
Entropy is a quantity for counting physical degrees of freedom in a system. At a finite temperature, one can use thermal entropy to study thermodynamical properties. At zero temperature, entanglement entropy is expected to provide a…
Many theoretical expressions of dissipation along non-equilibrium processes have been proposed. However, they have not been fully verified by experiments. Especially for systems strongly interacting with environments the connection between…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Whether a system is to be considered complex or not depends on how one searches for correlations. We propose a general scheme for calculation of entropies in lattice systems that has high flexibility in how correlations are successively…
In this letter we propose the use of physics techniques for entropy determination on constrained parameter optimization problems. The main feature of such techniques, the construction of an unbiased walk on energy space, suggests their use…
Entropy is one of the key thermodynamic variables reflecting changes in the state of matter. Unlike other thermodynamic variables, it is well-defined also for nonequilibrium steady states through its relation to information. Applying this…
We describe a novel method to obtain thermodynamic properties of quantum systems using Baysian Inference -- Maximum Entropy techniques. The method is applicable to energy values sampled at a discrete set of temperatures from Quantum Monte…
Nonequilibrium processes break time-reversal symmetry and generate entropy. Living systems are driven out-of-equilibrium at the microscopic level of molecular motors that exploit chemical potential gradients to transduce free energy to…
I propose a new algorithm, a free energy Monte Carlo algorithm, for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest version of the proposed algorithm allows for the determination of…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
We study entropy-bounded computational geometry, that is, geometric algorithms whose running times depend on a given measure of the input entropy. Specifically, we introduce a measure that we call range-partition entropy, which unifies and…