Related papers: Electrostatic interactions in concentrated protein…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
A subsystem approach for obtaining electron binding energies in the valence region and apply it to the case of halide ions (X$^-$, X = F-At) in water. This approach is based on electronic structure calculations combining the relativistic…
This work introduces novel unconditionally stable operator splitting methods for solving the time dependent nonlinear Poisson-Boltzmann (NPB) equation for the electrostatic analysis of solvated biomolecules. In a pseudo-transient…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Recently \1, we presented a general theory for calculat- ing the strength and properties of colloidal interactions mediated by ligand-receptor bonds (such as those that bind DNA-coated colloids). In this communication, we derive a…
Long-range electrostatic interactions critically affect polar materials. However, state-of-the-art atomistic potentials, such as neural networks or Gaussian approximation potentials employed in large-scale simulations, often neglect the…
We describe a self-contained procedure to evaluate the free energy of liquid and solid phases of an alloy system. The free energy of a single-element solid phase is calculated with thermodynamic integration using the Einstein crystal as the…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
A linear-response method to calculate the effective Coulomb interaction ($U$) between closed-shell localized electrons is suggested and applied to the $3d$ closed-shell systems (Cu, Zn, and ZnO) based on plane-wave basis density-functional…
In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it…
We consider an electrolyte solution confined by semipermeable membranes in contact with a salt-free solvent. Membranes are uncharged, but since small counter-ions leak-out into infinite salt-free reservoirs, we observe a distance-dependent…
The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the…
A melting transition for a system of hard spheres interacting by a repulsive Yukawa potential of DLVO form is studied. To find the location of the phase boundary, we propose a simple theory to calculate the free energies for the coexisting…
This letter describes a method for obtaining an explicit expression for the electrostatic energy of a charged elliptical infinitely thin disc. The charge distribution is assumed to be polynomial. Such explicit values for this energy are…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson-Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the…