Related papers: The lock and key model for Molecular Recognition. …

The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The…

Molecular Communications (MC) uses molecules as information carriers between nanomachines. MC channel in practice can be crowded with different types of molecules, i.e., ligands, which can have similar binding properties causing severe…

Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality…

Deep learning models have become fundamental tools in drug design. In particular, large language models trained on biochemical sequences learn feature vectors that guide drug discovery through virtual screening. However, such models do not…

A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance…

LLMs often default to equal treatment across cultural groups, even though context warrants differentiation: this is a lack of difference awareness. Using mechanistic interpretability and a factorial design on the N4 cultural appropriation…

The strength of a simple soft bond under constant loading rate is studied theoretically. We find a scaling regime where rebinding is negligible and the rupture force of the bond scales as $const. + (\ln (kv))^{2/3}$, where $kv$ is the…

While spin squeezing has been traditionally considered in all-to-all interacting models, recent works have shown that it can also occur in systems with power-law interactions, enabling direct tests in Rydberg atoms, trapped ions, ultracold…

Many biological systems fold thin sheets of lipid membrane into complex three-dimensional structures. This microscopic origami is often mediated by the adsorption and self-assembly of proteins on a membrane. As a model system to study…

We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…

A new particle - discovered recently with the Atlas and CMS detectors at LHC - has been interpreted as the long sought Higgs-boson. A corresponding scalar field is needed to make the weak interaction gauge invariant and to understand the…

We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…

The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize…

Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…

The interactions between acceptors in semiconductors are often treated in qualitatively the same manner as those between donors. Acceptor wave functions are taken to be approximately hydrogenic and the standard hydrogen molecule…

The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide…

Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge…

Using the model of hexagonal clusters we express the surface, curvature and Gauss curvature coefficients of the nuclear binding energy in terms of its bulk coefficient. Using the derived values of these coefficients and a single fitting…