Related papers: Using binding free energy to guide ligand design
The expression of the free energy of a liquid in terms of an explicit decomposition of the particle configurations into local coordination clusters is examined. We argue that the major contribution to the entropy associated with structural…
Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. The Coulomb interactions are emulated by harmonic repulsive forces, the force constants being…
We present a theory of unbinding transitions for membranes that interact via short and long receptor/ligand bonds. The detail of unbinding behavior of the membranes is governed by the binding energies and concentrations of receptors and…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
We compute the high-dimensional limit of the free energy associated with a multi-layer generalized linear model. Under certain technical assumptions, we identify the limit in terms of a variational formula. The approach is to first show…
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…
The free energy between a static quark and an antiquark is studied by using the color-singlet Polyakov-line correlation at finite temperature in lattice QCD with 2+1 flavors of improved Wilson quarks. From the simulations on $32^3 \times…
Based on large-scale Monte Carlo simulations on lattice the energy probability distribution functions are investigated for a large set of primary sequences in distinct models of copolymers at low temperatures below transitions to compacted…
The bootstrap method has proven useful for a wide range of matrix models. Here, we show that the computed momenta can be used to reconstruct the underlying eigenvalue probability distribution, which in turn allows us to compute the free…
In this manuscript, we describe a new configurational bias Monte Carlo technique for the simulation of peptides. We focus on the biologically relevant cases of linear and cyclic peptides. Our approach leads to an efficient,…
The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is well-established, yet somewhat complex, with counter-intuitive aspects. This leads to frequent frustration, common…
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also…
Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the…
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,…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid…
Quantum Monte Carlo methods have recently been employed to study properties of nuclei and infinite matter using local chiral effective field theory interactions. In this work, we present a detailed description of the auxiliary field…
We describe a simple Monte Carlo simulation method to calculate the free-energy cost of localizing a single monomer of a polymer confined to a cavity. The localization position is chosen to be on the inside surface of the confining cavity.…
We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…