Related papers: Binding memory of liquid molecules
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Memory effects are ubiquitous in nature and are particularly relevant at the nanoscale where the dynamical properties of electrons and ions strongly depend on the history of the system, at least within certain time scales. We review here…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Memory is often defined as the mental capacity of retaining information about facts, events, procedures and more generally about any type of previous experience. Memories are remembered as long as they influence our thoughts, feelings, and…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Microscopic understanding of liquid properties is essential for advancing a wide range of applications from energy applications such as nuclear reactors and batteries to biomedical applications including drug delivery and microfluidics.…
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Memory effects in time-series of experimental observables are ubiquitous, have important cosequences for the interpretation of kinetic data, and may even affect the function of biomolecular nanomachines such as enzymes. Here we propose a…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
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…
In the mammalian brain, newly acquired memories depend on the hippocampus for maintenance and recall, but over time the neocortex takes over these functions, rendering memories hippocampus-independent. The process responsible for this…
The search for universal laws that help establish a relationship between dynamics and computation is driven by recent expansionist initiatives in biologically inspired computing. A general setting to understand both such dynamics and…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides and antibodies. Notably, drug molecule residence time or…