Related papers: Using binding free energy to guide ligand design
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
Quantum Monte Carlo methods are used to calculate various ground state properties of charged bosons in two dimensions, throughout the whole density range where the fluid phase is stable. Wigner crystallization is predicted at $r_s\simeq…
Exact free energy minimization is a convex optimization problem that is usually approximated with stochastic sampling methods. Deterministic approximations have been less successful because many desirable properties have been difficult to…
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…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
The entropy per particle in most Monte-Carlo simulations is size dependent due to correlated energy fluctuations. Guided by nanothermodynamics, we find a constraint for the Ising model that enhances the fluctuations and lowers the free…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We propose a new approach, "structure integration", enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based…
I propose a new algorithm, a free energy Monte Carlo algorithm, for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest version of the proposed algorithm allows for the determination of…
We investigate the phenomenon of protein induced tubulation of lipid bilayer membranes within a continuum framework using Monte Carlo simulations coupled with the Widom insertion technique to compute excess chemical potentials. Tubular…
Machine learning is used to approximate the kinetic energy of one dimensional diatomics as a functional of the electron density. The functional can accurately dissociate a diatomic, and can be systematically improved with training. Highly…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
Monte Carlo simulations are used to study the magnetic relaxation of a system of single domain particles with dipolar interactions modeled by a chain of Heisenberg classical spins. We show that the so-called $T\ln(t/\tau_0)$ method can be…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
For one-dimensional spin and pseudospin models that allow mapping to a Markov chain, the free energy of the system at a finite temperature can be expressed in terms of bond concentrations. Minimizing the free energy function makes it…
A method for computing the thermopower in interacting systems is proposed. This approach, which relies on Monte Carlo simulations, is illustrated first for a diatomic chain of hard-point elastically colliding particles and then in the case…