相关论文: VDAC Solvation Free Energy Calculation by a Nonuni…
In this paper, a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) model is presented as a nonlinear system of an electrostatic potential and multiple ionic concentrations. It mixes nonlinear algebraic equations with a…
This paper presents an efficient finite element iterative method for solving a nonuniform size-modified Poisson-Nernst-Planck ion channel (SMPNPIC) model, along with a SMPNPIC program package that works for an ion channel protein with a…
The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as…
Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a…
We explore the recently introduced $\eta$-ensemble approach to compute the free energy directly from \emph{ab initio} path integral Monte Carlo (PIMC) simulations [T.~Dornheim \emph{et al.}, arXiv:2407.01044] and apply it to the archetypal…
Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…
ariational implicit solvation models (VISM) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
We present a modified Poisson-Boltzmann model that adds steric repulsion of ions, providing an approximation to ion-ion correlations. Controlled by specific ion sizes, this steric contribution provides a concentration cap. Importantly, the…
A recently developed statistical mechanical Quasi-Chemical Theory (QCT) has led to significant insights into solvation phenomena for both hydrophilic and hydrophobic solutes. The QCT exactly partitions solvation free energies into three…
ADAPT-VQE stands out as a robust algorithm for constructing compact ans\"atze for molecular simulation. It enables to significantly reduce the circuit depth with respect to other methods, such as UCCSD, while achieving higher accuracy and…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
The energy functional, the governing partial differential equation(s) (PDE), and the boundary conditions need to be consistent with each other in a modeling system. In electrolyte solution study, people usually use a free energy form of an…
The interacting quantum Bose gas is a random ensemble of many Brownian bridges (cycles) of various lengths with interactions between any pair of legs of the cycles. It is one of the standard mathematical models in which a proof for the…
A model of a finite cylindrical ion channel through a phospholipid membrane of width $L$ separating two electrolyte reservoirs is studied. Analytical solution of the Poisson equation is obtained for an arbitrary distribution of ions inside…
Free energy perturbation (FEP) is considered the gold-standard simulation method for estimating small molecule binding affinity, a quantity of vital importance to drug discovery. The accuracy of FEP critically depends on an accurate model…
The absolute-scale electronic energetics of liquid water and aqueous solutions, both in the bulk and at associated interfaces, are the central determiners of water-based chemistry. However, such information is generally experimentally…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity.…