Related papers: A Rational Method for Probing Macromolecules Disso…
Compressible Mooney-Rivlin theory has been used to model hyperelastic solids, such as rubber and porous polymers, and more recently for the modeling of soft tissues for biomedical tissues, undergoing large elastic deformations. We propose a…
We study the adsorption and desorption kinetics of interacting particles moving on a one-dimensional lattice. Confinement is introduced by limiting the number of particles on a lattice site. Adsorption and desorption are found to proceed at…
Complex microscopic many-body processes are often interpreted in terms of so-called `reaction coordinates', i.e. in terms of the evolution of a small set of coarse-grained observables. A rigorous method to produce the equation of motion of…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
This Chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full…
In the study of relaxation processes in coherent non-equilibrium dynamics of quenched quantum systems, ultracold atoms in optical superlattices with periodicity two provide a very fruitful test ground. In this work, we consider the dynamics…
The Linearized Poisson--Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article we derive the analytical forces of the…
We propose a strategy for enabling photodissociation of a normally photostable molecule through coupling to a nanoparticle plasmon. The large possible coupling on the single-molecule level combined with the highly lossy nature of plasmonic…
The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) tools for drug-protein interaction studies, existing training…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
We propose a variational splitting technique for the generalized-$\alpha$ method to solve hyperbolic partial differential equations. We use tensor-product meshes to develop the splitting method, which has a computational cost that grows…
We present theoretical work in which the degree of electrostatic coupling across a charged lipid bilayer in aqueous solution is analyzed on the basis of nonlinear Poisson-Boltzmann theory. In particular, we consider the electrostatic…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…
We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides…