Related papers: Computing equilibrium free energies through a none…
A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and non-equilibrium…
We introduce an algorithm for sampling many-body quantum states in Fock space. The algorithm efficiently samples states with probability approximately proportional to an arbitrary function of the second-quantized Hamiltonian matrix element…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
In many quantum quench experiments involving cold atom systems the post-quench system can be described by a quantum field theory of free scalars or fermions, typically in a box or in an external potential. We work with free scalars in…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
Energy-Based Models (EBMs) present a flexible and appealing way to represent uncertainty. Despite recent advances, training EBMs on high-dimensional data remains a challenging problem as the state-of-the-art approaches are costly, unstable,…
This study examines a new formulation of non-equilibrium thermodynamics, which gives a conditional derivation of the ``maximum entropy production'' (MEP) principle for flow and/or chemical reaction systems at steady state. The analysis uses…
In order to predict the potential energy surface (PES) from measured structure in equilibrium state, one should typically perform trial-and-error statistical thermodynamic simulation with assumed multibody interactions. Very recently, we…
Bayesian models have many desirable properties, most notable is their ability to generalize from limited data and to properly estimate the uncertainty in their predictions. However, these benefits come at a steep computational cost as…
A simple theoretical approach is used to investigate active colloids at the free interface and near repulsive substrates. We employ dynamical density functional theory to determine the steady-state density profiles in an effective…
We study, both theoretically and numerically, the equilibrium of a hinged rigid leaflet with an attached rotational spring, immersed in a stationary incompressible fluid within a rigid channel. Through a careful investigation of the…
In Bayesian statistics, exploring high-dimensional multimodal posterior distributions poses major challenges for existing MCMC approaches. This paper introduces the Annealed Leap-Point Sampler (ALPS), which augments the target distribution…
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation…
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…
We present a temperature-independent Monte Carlo method for the determination of the density of states of lattice proteins that combines the fast ground-state search strategy of the nPERM chain growth and multicanonical reweighting for…
We propose a numerical technique to compute the equilibrium free energy of glasses that cannot be prepared quasi-reversibly. For such systems, standard techniques for estimating the free energy by extrapolation, cannot be used. Instead, we…
We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core…
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational cost of multidimensional sampling. In this work, we extend…
We study the out-of-equilibrium behavior of statistical systems along critical relaxational flows arising from instantaneous quenches of the temperature $T$ to the critical point $T_c$, starting from equilibrium conditions at time $t=0$. In…
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…