相关论文: A "fast growth" method of computing free energy di…
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…
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…
Nonequilibrium, ``fast switching'' estimates of equilibrium free energy differences, Delta F, are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced…
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…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
Time evolution of quantum systems is accelerated by the fast-forward scaling. We reformulate the method to study systems in a finite-dimensional Hilbert space. For several simple systems, we explicitly construct the acceleration potential.…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means…
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…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences (DF) between two states or systems are critically important…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
We give an algorithm that computes the final state of certain growth models without computing all intermediate states. Our technique is based on a "least action principle" which characterizes the odometer function of the growth process.…
For over two decades, Flux Balance Analysis (FBA) has been successfully used for predicting growth rates and intracellular reaction rates in microbiological metabolism. An aspect that is often omitted from this analysis, is segregation or…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting…
We numerically study the metastable states of the 2d Potts model. Both of equilibrium and relaxation properties are investigated focusing on the finite size effect. The former is investigated by finding the free energy extremal point by the…
The energy method can be used to identify well-posed initial boundary value problems for quasi-linear, symmetric hyperbolic partial differential equations with maximally dissipative boundary conditions. A similar analysis of the discrete…
The rate of the trace distance is used to evaluate quantum speed-up for arbitrary mixed states. Compared with some present methods, the approach based on trace distance can provide an optimal bound to the speed of the evolution. The…
We propose energy-saving fast-forward scaling. Fast-forward scaling is a method which enables us to speed up (or slow down) given dynamics in a certain measurement basis. We introduce energy costs of fast-forward scaling, and find…