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The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the…
We report first principles ab initio density functional calculations of hydrogen dynam- ics in hydrogenated amorphous silicon. Thermal motion of the host Si atoms drives H diffusion, as we demonstrate by direct simulation and explain with…
Using first principles simulations we have investigated the structural and bonding properties of dense fluid oxygen up to 180 GPa. We have found that band gap closure occurs in the molecular liquid, with a "slow" transition from a…
The Diels-Alder reaction between 2,3-dibromo-1,3-butadiene and maleic anhydride has been studied by means of multisurface adiabatic reactive molecular dynamics and the PhysNet neural network architecture. This system is used as a prototype…
Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics…
We present a detailed analysis of rho(0) electroproduction at intermediate energy for quasi-elastic knockout kinematics. The approach is based on an effective Lagrangian which generates exchanges of scalar, pseudoscalar, axial-vector and…
Simulated sliding between an oxidized silicon tip and surface over six decades of velocity using accelerated molecular dynamics reproduces the experimentally observed velocity dependence of the friction force. Unlike in the crystalline…
We consider a lattice model for three-component systems in which the lattice bonds are covered by molecules of type AA, BB, and AB, and the only interactions are between the molecular ends of a common lattice site. The model is equivalent…
Using an \textit{ab initio} approach based on the GW approximation which includes strong local \textbf{k}-space correlations, the Metal-Insulator Transition of M$_2$ vanadium dioxide is broken down into its component parts and investigated.…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
The role of the hard Pomeron (HP) exchanges in the high-energy diffractive interaction of nucleons is explored. It is demonstrated that the HP subdominance at available energies and low transferred momenta is due to the extremely low slope…
The interface chemistry of silicon nanocrystals (NCs) embedded in amorphous oxide matrix is studied through molecular dynamics simulations with the chemical environment described by the reactive force field model. Our results indicate that…
Interstellar and cometary ices play an important role in the formation of planetary systems around young stars. Their main constituent is amorphous solid water (ASW). Although ASW is widely studied, vibrational energy dissipation and…
Apart from the most studied tin-oxide compounds, SnO and SnO2, intermediate states have been claimed to exist for more than a hundred years. In addition to the known homologous series (Seko et al., Phys. Rev. Lett. 100, 045702 (2008)), we…
We develop the multi-scale ab-initio scheme for correlated electrons (MACE) for transitionmetal-oxide heterostructures, and determine the parameters of the low-energy effective model. By separating Ti t2g bands near the Fermi level from the…
The hydrogen-bond (H-bond) network of high-pressure water is investigated by neural-network-based molecular dynamics (MD) simulations with the first-principles accuracy. The static structure factors (SSFs) of water at three densities, i.e.,…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray…
We present a mathematically rigorous method suitable for solving three-body bound state and scattering problems when the inter-particle interaction is of a hard-core nature. The proposed method is a variant of the Boundary Condition Model…