Related papers: Simultaneous identification of multiple binding si…
In this chapter we review the electrostatic properties of charged membranes in aqueous solutions, with or without added salt, employing simple physical models. The equilibrium ionic profiles close to the membrane are governed by the…
We consider diffusion of independent molecules in an insulated Euclidean domain with unknown diffusivity parameter. At a random time and position, the molecules may bind and stop diffusing in dependence of a given `binding potential'. The…
Active proteins and membrane-bound motors exert force dipole flows along fluid interfaces and lipid bilayers. We develop a Hamiltonian framework for the interactions of pusher and puller dipoles embedded in an incompressible two-dimensional…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
The interplay of phase separation and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as hard and soft condensed matter physics, materials science, food engineering and…
We present a model for the joint self-assembly of amphiphilic polymers and small amphiphilic molecules (surfactants) in a dilute aqueous solution. The polymer is assumed to consist of a hydrophilic backbone and a large number of hydrophobic…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
In this paper, we first develop a mathematical model for long-range, hydrophobic attraction between amphiphilic particles. The non-pairwise interactions follow from the first variation of a hydrophobic attraction domain functional. The…
This application paper investigates the stability of hydrogen bonds (H-bonds), as characterized by the Quantum Theory of Atoms in Molecules (QTAIM). First, we contribute a database of 4544 electron densities associated to four isomers of…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affect hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size…
We use a lattice Boltzmann method to study pattern formation in chemically reactive binary fluids in the regime where hydrodynamic effects are important. The coupled equations solved by the method are a Cahn-Hilliard equation, modified by…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
This review focuses on the striking recent progress in solving for hydrophobic interactions between small inert molecules. We discuss several new understandings. Firstly, the _inverse _temperature phenomenology of hydrophobic interactions,…
Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…
An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on…
We show that hydrophilic ions present in a confined, near-critical aqueous mixture can lead to an attraction between like charge surfaces with opposing preferential adsorption of the two species of the mixture, even though the corresponding…
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…
The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…
Predicting protein-ligand binding affinity remains intractable for multi-domain proteins, where inter-domain dynamics govern molecular recognition. Existing geometric deep learning methods typically treat proteins as monolithic static…