Related papers: High-throughput Binding Affinity Calculations at E…
We introduce ABEL, the Adaptable Beginning-to-End Linac simulation framework developed for agile design studies of plasma-based accelerators and colliders. ABEL's modular architecture allows users to simulate particle acceleration across…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
Ligand strain energy, the energy difference between the bound and unbound conformations of a ligand, is an important component of structure-based small molecule drug design. A large majority of observed ligands in protein-small molecule…
The linear combination of atomic orbitals (LCAO) is a standard method for studying solids and molecules, it is also known as the tight$-$binding (TB) method. In most of the implementations only the basis set and the coupling constants are…
Forming a hetero-interface is a materials-design strategy that can access an astronomically large phase space. However, the immense phase space necessitates a high-throughput approach for optimal interface design. Here we introduce a…
Multidrug resistance consists of a series of genetic and epigenetic alternations that involve multifactorial and complex processes, which are a challenge to successful cancer treatments. Accompanied by advances in biotechnology and…
Determining a process-structure-property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials…
The DCA$^+$ algortihm was recently introduced to extend the dynamic cluster approximation (DCA) with a continuous lattice self-energy in order to achieve better convergence with cluster size. Here we extend the DCA$^+$ algorithm to the…
A challenge - and opportunity - is offered to the Hubbard Model community of solutions extant for the strong coupling region. A rigorous and quantitatively demanding test - a Computer Lab - is presented based on certain exact results for…
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…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
The high computational cost of ab-initio methods limits their application in predicting electronic properties at the device scale. Therefore, an efficient method is needed to map the atomic structure to the electronic structure quickly.…
Test-Time Adaptation (TTA) has recently emerged as a promising approach for tackling the robustness challenge under distribution shifts. However, the lack of consistent settings and systematic studies in prior literature hinders thorough…
Relative Binding Free Energy (RBFE) calculations are a cornerstone of rational hit-to-lead and lead optimization in modern drug discovery. However, the high computational cost and limited reliability in tackling large or complex molecular…
The development of new manufacturing techniques such as 3D printing have enabled the creation of previously infeasible chemical reactor designs. Systematically optimizing the highly parameterized geometries involved in these new classes of…
This paper advocates for an innovative approach designed for estimating optoelectronic properties of quantum structures utilizing Tight-Binding (TB) theory. Predicated on the comparative analysis between estimated and actual properties, the…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…