Related papers: Using Metadynamics to Reveal Extractant Conformati…
The normal modes and relaxation rates of weak colloidal gels are investigated in computations employing different models of the hydrodynamic interactions between colloids. The eigenspectrum is computed for freely draining,…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Contraction analysis establishes exponential incremental convergence of a nonlinear system by solving a linear matrix inequality for a contraction metric, and has become a standard resource for solving problems in nonlinear control and…
We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue…
An innovative and accurate dynamic Compact Thermal Model extraction method is proposed for multi-chip power electronics systems. It accounts for thermal coupling between multiple heat sources. Transient electro-thermal coupling can easily…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
Alchemical free energy calculations are widely used in predicting pKa, and binding free energy calculations in biomolecular systems. These calculations are carried out using either Free Energy Perturbation (FEP) or Thermodynamic Integration…
We analyze a model problem representing a multi-electronic molecule sitting on a metal surface. Working with a reduced configuration interaction Hamiltonian, we show that one can extract very accurate ground state wavefunctions as compared…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
An expansion of energy characteristics of wide thin slab of thickness L in power of 1/L is constructed using the free-electron approximation and the model of a potential well of finite depth. Accuracy of results in each order of the…
Machine learning force fields (MLFFs) promise to accurately describe the potential energy surface of molecules at the ab initio level of theory with improved computational efficiency. Within MLFFs, equivariant graph neural networks (EQNNs)…
The current catalyst discovery and development pipeline for energy-intensive applications like methane conversion remains bottlenecked by expensive trial-and-error experimentation, irreproducible chemical intuition, and a lack of frameworks…
Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current…
In the present study we investigate magnetic reconnection in twisted magnetic fluxtubes with different initial configurations. In all considered cases, energy release is triggered by the ideal kink instability, which is itself the result of…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…
Off-diagonal profiles of local densities (e.g. order parameter or energy density) are calculated at the bulk critical point, by conformal methods, for different types of boundary conditions (free, fixed and mixed). Such profiles, which are…
Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented by using localized basis sets of reduced size, leaving no…
The phase diagram of the ferromagnetic Kondo model for manganites is investigated using computational techniques. In clusters of dimensions 1 and 2, Monte Carlo simulations in the limit where the localized spins are classical show a rich…