相关论文: Single-ensemble nonequilibrium path-sampling estim…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in…
Scenario reduction techniques are widely applied for solving sophisticated dynamic and stochastic programs, especially in energy and power systems, but also used in probabilistic forecasting, clustering and estimating generative adversarial…
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 study the high-dimensional limit of the free energy associated with the inference problem of a rank-one nonsymmetric matrix. The matrix is expressed as the outer product of two vectors, not necessarily independent. The distributions of…
We study the accuracy of analytical wave function based many-body methods derived by energy minimization of a Jastrow-Feenberg ansatz for electrons (`Fermi hypernetted chain / Euler Lagrange' approach). Approximations to avoid the…
We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic thermodynamics. The first example is the…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
The well-known Jarzynski equality, often written in the form $e^{-\beta\Delta F}=\langle e^{-\beta W}\rangle$, provides a non-equilibrium means to measure the free energy difference $\Delta F$ of a system at the same inverse temperature…
We generalize a recently developed method for accelerated Monte Carlo calculation of path integrals to the physically relevant case of generic many-body systems. This is done by developing an analytic procedure for constructing a hierarchy…
The unconstrained ensemble describes completely open systems whose control parameters are chemical potential, pressure, and temperature. For macroscopic systems with short-range interactions, thermodynamics prevents the simultaneous use of…
The shift in chemical equilibria due to isotope substitution is often exploited to gain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using…
We experimentally realize protocols that allow to extract work beyond the free energy difference from a single electron transistor at the single thermodynamic trajectory level. With two carefully designed out-of-equilibrium driving cycles…
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential.…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Modern randomization methods in clinical trials are invariably adaptive, meaning that the assignment of the next subject to a treatment group uses the accumulated information in the trial. Some of the recent adaptive randomization methods…
For a 2-dimensional freely jointed chain with 3 particles and a related model, the average and variance of the kinetic energies of each particle in thermal equilibrium are exactly obtained. The same is done for a related model. The excess…
We consider the statistical mechanics of a classical particle in a one-dimensional box subjected to a random potential which constitutes a Wiener process on the coordinate axis. The distribution of the free energy and all correlation…
An innovative and accurate dynamic Compact Thermal Model extraction method is proposed for multi-chip power electronics systems. It accounts for thermal coupling between multiple heat sources. Transient electro-thermal coupling can easily…