相关论文: Ligand Discrimination in Myoglobin from Linear-Sca…
Two-dimensional (2d) nano-electronics, plasmonics, and emergent phases require clean and local charge control, calling for layered, crystalline acceptors or donors. Our Raman, photovoltage, and electrical conductance measurements combined…
We study water between parallel metal walls under applied electric field accounting for the image effect at $T=298$ K. The electric field due to the surface charges serves to attract and orient nearby water molecules, while it tends to a…
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component…
Predicting the compositional phase stability of strongly correlated electron materials is an outstanding challenge in condensed matter physics. In this work, we employ the DFT+U formalism to address the effects of local correlations due to…
An ab initio study of the electronic and spin configuration for the iron ion in the active center of the human hemoglobin molecule is presented. It is well known that the iron ion, being surrounded by the porphyrin ring and the ligands,…
We present a method which uses density functional theory (DFT) to treat transport through a single molecule connected to two conducting leads for the weak and intermediate coupling. This case is not accessible to standard non-equilibrium…
Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…
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…
The present manuscript revisits one of the earliest approaches to treating molecular systems within the Schr\"odinger formalism of quantum mechanics: the Heitler-London (HL) model. Originally proposed in 1927 and based on a linear…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
Rotational friction on proteins and macromolecules is known to derive contributions from at least two distinct sources -- hydrodynamic (due to viscosity) and dielectric friction (due to polar interactions). In the existing theoretical…
Diamond-like carbon (DLC) films are synthesized on Si using plasma enhanced chemical vapor deposition. The role of substrate bias and nitrogen doping on the structural evolution and local elastic modulus of DLC films are systematically…
Many different processes take place to facilitate lubrication of the joints functioning in human locomotion system. The main purpose of this is to avoid destroying the articular cartilage. Viscoelastic properties of the joints system are…
We propose a self-consistent site-dependent Hubbard $U$ approach for DFT+$U$ calculations of defects in complex transition-metal oxides, using Hubbard parameters computed via linear-response theory. The formation of a defect locally…
We investigate the effects of inhomogeneities on spin entanglement in many-electron systems from an ab-initio approach. The key quantity in our approach is the local spin entanglement length, which is derived from the local concurrence of…
Combining the bond-order-length-strength (BOLS) and bonding and binding energy (BB) models with density functional theory (DFT) calculations, we studied the atomic bonding and binding energy behavior of Bi atoms adsorbed on the Li(110)…
Ranking the binding of small molecules to protein receptors through physics-based computation remains challenging. Though inroads have been made using free energy methods, these fail when the underlying classical mechanical force fields are…
The density functional theory (DFT)+$U$ method is a pragmatic and effective approach for calculating the ground-state properties of strongly-correlated systems, and linear response calculations are widely used to determine the requisite…
We present a DFT+U-type functional for strong correlation, derived from multiconfigurational wavefunction theory. The reference system experiences electron-electron interactions only in DFT+U-type atomic states, yielding a block-localized…
Understanding the electronic properties of dopants near an interface is a critical challenge for nano-scale devices. We have determined the effect of dielectric mismatch and quantum confinement on the ionization energy of individual…