Related papers: Determining Free Energy Differences Through Variat…
This paper is committed to investigate an extension of the classical adaptive biasing force method, which is used to compute the free energy related to the Boltzmann-Gibbs measure and a reaction coordinate function. The issue of this…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
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…
Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynamics the free-energy surface is filled by the addition of…
Soft porous crystals are flexible metal-organic frameworks that respond to physical stimuli such as temperature, pressure, and gas adsorption by large changes in their structure and unit cell volume. While they have attracted a lot of…
We present an accurate equation of state for water based on a simple microscopic Hamiltonian, with only four parameters that are well-constrained by bulk experimental data. With one additional parameter for the range of interaction, this…
We introduce and analyze free energy landscapes defined by associating to any point inside the sphere a free energy calculated on a thin spherical band around it, using many orthogonal replicas. This allows us to reinterpret, rigorously…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
We present a new description of the known large deviation function of the classical symmetric simple exclusion process by exploiting its connection with the quantum symmetric simple exclusion processes and using tools from free probability.…
Effective harmonic methods allow for calculating temperature dependent phonon frequencies by incorporating the anharmonic contributions into an effective harmonic Hamiltonian. The systematic errors arising from such an approximation are…
We investigate the energy transfer dynamics in a donor-acceptor model by developing a time-local master equation technique based on a variational transformation of the underlying Hamiltonian. The variational transformation allows a…
The calculation of the natural lineshape of an excited two-level atom (TLA) has long been known to be gauge-dependent, with certain experiments in better agreement with the lineshape calculated with the dipole gauge. We show that by using a…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
We propose a quantum algorithm to compute low-energy expectation values of a quantum Hamiltonian by sampling a partition function associated with the average energy of that Hamiltonian. For any given quantum circuit-Hamiltonian pair, there…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test system, the new (minimally optimized) method performs roughly one…
We developed a deep generative model-based variational free energy approach to the equations of state of dense hydrogen. We employ a normalizing flow network to model the proton Boltzmann distribution and a fermionic neural network to model…