Related papers: Absolute FKBP binding affinities obtained via non-…
We describe the representation of the chemical affinity between the antigen-combining site of the immunoglobulin molecule and the antigen molecule as the probability of the two molecules existing in a bound state. Our model is based on the…
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…
With the advent of digital and analog quantum simulation experiments, it is now possible to experimentally simulate dynamics of quantum many-body lattice systems and make site-resolved measurements. These experiments make it pertinent to…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
The limitation on obtaining precise outcomes of measurements performed on two non-commuting observables of a particle as set by the uncertainty principle in its entropic form, can be reduced in the presence of quantum memory. We derive a…
Electronic quantum entanglement between the central chain and the two electrodes in an infinite one-dimensional two-probe device system is studied. The entanglement entropy is calculated employing the nonequilibrium Green's function method…
We introduce a new class of machine learning interatomic potentials - fast General Two- and Three-body Potential (GTTP), which is as fast as conventional empirical potentials and require computational time that remains constant with…
A theoretical description for the radial density profile of a finite number of identical charged particles confined in a harmonic trap is developed for application over a wide range of Coulomb coupling (or, equivalently, temperatures) and…
There is now a rapidly growing body of experimental data relevant to the question of whether the standard model CKM quark mixing matrix is a correct description of \CP-violation as well as of non--\CP-violating flavor decay processes. In…
Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such…
We describe a systematic approach to generating approximate actions for the lattice simulation of QCD. Three different tuning conditions are defined to match approximate with true actions, and it is shown that these three conditions become…
Ligand-receptor interactions are fundamental to many biological processes. For example in antibody-based immunotherapies, the dynamics of an antibody binding with its target antigen directly influence the potency and efficacy of monoclonal…
Uncertainty relations lie at the very core of quantum mechanics, and form the cornerstone of essentially all quantum cryptographic applications. In particular, they play an important role in cryptographic protocols in the…
We present a GPU-friendly framework for real-time implicit simulation of elastic material in the presence of frictional contacts. The integration of hyperelasticity, non-interpenetration contact, and friction in real-time simulations…
The ability to selectively measure, initialize, and reuse qubits during a quantum circuit enables a mapping of the spatial structure of certain tensor-network states onto the dynamics of quantum circuits, thereby achieving dramatic resource…
We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between…
This study assesses the efficiency of several popular machine learning approaches in the prediction of molecular binding affinity: CatBoost, Graph Attention Neural Network, and Bidirectional Encoder Representations from Transformers. The…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the protein's thermal fluctuations, including both the large scale…