Related papers: Configurational space discretization and free ener…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Entropy governs molecular self-assembly, phase transitions, and material stability, yet remains challenging to quantify and directly control in molecular systems. Here, we demonstrate that the computable information density (CID), a data…
The configurational entropy is an indispensable tool to describe super-cooled liquids near the glass transition. Its calculation requires the enumeration of the basins in the potential energy landscape and when available, it reveals a…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
This paper provides a compositional scheme based on dissipativity approaches for constructing finite abstractions of continuous-time continuous-space stochastic control systems. The proposed framework enjoys the structure of the…
Atmospheric systems incorporating thermal dynamics must be stable with respect to both energy and entropy. While energy conservation can be enforced via the preservation of the skew-symmetric structure of the Hamiltonian form of the…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
This paper is concerned with a compositional approach for constructing both infinite (reduced-order models) and finite abstractions (a.k.a. finite Markov decision processes (MDPs)) of large-scale interconnected discrete-time stochastic…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
Numerical models of weather and climate critically depend on long-term stability of integrators for systems of hyperbolic conservation laws. While such stability is often obtained from (physical or numerical) dissipation terms, physical…
Self-organization creates new order and shifts sub-boundaries while reorganizing energy and entropy within a control volume. This article examines pathway selection and tests whether maximizing the entropy generation rate can forecast…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
We connect the configurational entropy of a liquid to the geometrical properties of its local energy landscape, using a high-temperature expansion. It is proposed that correlations between local structures arises from their overlap and,…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Accurate characterization of entropy plays a pivotal role in capturing reversible and irreversible heating in supercapacitors during charging/discharging cycles. However, numerical methods that can faithfully capture entropy variation in…
Depending on context, the term entropy is used for a thermodynamic quantity, a~measure of available choice, a quantity to measure information, or, in the context of statistical inference, a maximum configuration predictor. For systems in…
This study proposes a novel spatial discretization procedure for the compressible Euler equations which guarantees entropy conservation at a discrete level when an arbitrary equation of state is assumed. The proposed method, based on a…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical…
The paper analyzes the entropy of a system composed by non-interacting and indistinguishable particles whose quantum state numbers are modelled as independent and identically distributed classical random variables. The crucial observation…