Related papers: Binding memory of liquid molecules
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The…
Soft materials are not only highly deformable but they also possess rich and diverse body dynamics. Soft body dynamics exhibit a variety of properties, including nonlinearity, elasticity, and potentially infinitely many degrees of freedom.…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
Continuous, adaptive learning, the ability to adapt to the environment and keep improving performance, is a hallmark of natural intelligence. Biological organisms excel in acquiring, transferring, and retaining knowledge while adapting to…
We simulate static memory materials on a two-dimensional lattice. The bulk properties of such materials depend on boundary conditions. Considerable information can be stored in various local patterns. We observe local probabilities…
Single receptor-ligand bonds have finite lifetimes, so that biological systems can dynamically react to changes in their environment. In cell adhesion, adhesion bonds usually act cooperatively in adhesion clusters. Outside the cellular…
We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We find that bond lifetime (``fast dynamics'') has Arrhenius temperature dependence. We also calculate the bond correlation function…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
Memory effects can lead to history-dependent behavior of a system, and they are ubiquitous in our daily life and have broad applications. Here we explore possibilities of generating memory effects in simple isolated quantum systems. By…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
The motion of an optically trapped sphere constrained by the vicinity of a wall is investigated at times where hydrodynamic memory is significant. First, we quantify, in bulk, the influence of confinement arising from the trapping potential…
Firing rate models are dynamical systems widely used in applied and theoretical neuroscience to describe local cortical dynamics in neuronal populations. By providing a macroscopic perspective of neuronal activity, these models are…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
We present a study of the spreading of liquid droplets on a solid substrate at very small scales. We focus on the regime where effective wetting energy (binding potential) and surface tension effects significantly influence steady and…