Related papers: Theory of Systematic Computational Error in Free E…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the availability of only a finite number of data values, N. In…
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's…
Computational models in chemistry rely on a number of approximations. The effect of such approximations on observables derived from them is often unpredictable. Therefore, it is challenging to quantify the uncertainty of a computational…
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 study nonequilibrium properties of small and chaotic quantum systems, i.e., non-integrable systems whose size is small in the sense that the separations of energy levels are non-negligible as compared with other relevant energy scales.…
The Free Energy Principle (FEP) states that under suitable conditions of weak coupling, random dynamical systems with sufficient degrees of freedom will behave so as to minimize an upper bound, formalized as a variational free energy, on…
In QM/MM indirect free energy simulation, QM/MM corrections can be obtained from integration of partial derivatives of alchemical Hamiltonians or from perturbation-based estimators including free energy perturbation (FEP) and acceptance…
The difference Delta F between free energies has applications in biology, chemistry, and pharmacology. The value of Delta F can be estimated from experiments or simulations, via fluctuation theorems developed in statistical mechanics.…
We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results suggest that extrapolation can greatly reduce the systematic…
For the theoretical understanding of the reactivity of complex chemical systems accurate relative energies between intermediates and transition states are required. Despite its popularity, density functional theory (DFT) often fails to…
Bayesian inference is a widely used statistical method. The free energy and generalization loss, which are used to estimate the accuracy of Bayesian inference, are known to be small in singular models that do not have a unique optimal…
A unified treatment for the existence of free energy in several random energy models is presented. If the sequence of distributions associated with the particle systems obeys a large deviation principle, then the free energy exists almost…
We study the effects of dynamical imperfections in quantum computers. By considering an explicit example, we identify different regimes ranging from the low-frequency case, where the imperfections can be considered as static but with…
The free-energy difference $\Delta F$ between two high-dimensional systems is notoriously difficult to compute, but very important for many applications, such as drug discovery. We demonstrate that an unconventional definition of work…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
We derive the fluctuation theorem for quantum-state statistics that can be obtained when we initially measure the total energy of a quantum system at thermal equilibrium, let the system evolve unitarily, and record the quantum-state data…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
Is perfect error correction always worth the trouble? A framework is presented for the analysis of error detection and correction in multi-level systems of communication that takes into account degrees of freedom attended and ignored by…
We obtain error rates for large deviations of sums of i.i.d. random variables in, a particular case, of the domain of a non-symmetric infinite mean $\alpha=1$-stable law. The focus of this work is on the method of proof via analytic…
We consider a quantum system with $N$ degrees of freedom which is classically chaotic. When $N$ is large, and both $\hbar$ and the quantum energy uncertainty $\Delta E$ are small, quantum chaos theory can be used to demonstrate the…