Related papers: Binding memory of liquid molecules
Many practically relevant materials combine properties of viscous fluids and elastic solids to viscoelastic behavior. Our focus is on the induced dynamic behavior of damped finite-sized particulate inclusions in such substances. We…
The origin of the dramatic changes in the behavior of liquids as they approach their vitreous state - increases of many orders of magnitude in transport properties and dynamic time scales - is a major unsolved problem in condensed matter.…
Cells attach to their environment by means of focal adhesions, which are molecular complexes that exhibit the remarkable ability to adapt to mechanical load by changing their size. Drawing from the biomolecular mechanisms underlying this…
Solids are rigid, which means that when left undisturbed, their structures are nearly static. It follows that these structures depend on history -- but it is surprising that they hold readable memories of past events. Here we review the…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
As LLM-based agents are increasingly used in long-term interactions, cumulative memory is critical for enabling personalization and maintaining stylistic consistency. However, most existing systems adopt an ``all-or-nothing'' approach to…
In the mammalian brain newly acquired memories depend on the hippocampus for maintenance and recall, but over time these functions are taken over by the neocortex through a process called systems consolidation. However, reactivation of a…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Adhesion plays an integral role in diverse biological functions ranging from cellular transport to tissue development. Estimation of adhesion strength, therefore, becomes important to gain biophysical insight into these phenomena. In this…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
The dynamics and deformations of immersed flexible fibers are at the heart of important industrial and biological processes, induce peculiar mechanical and transport properties in the fluids that contain them, and are the basis for novel…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
We investigate the memory effects under oscillatory shear deformation of amorphous solids through computer simulations. Applications of shear deformations in all orthogonal directions show that encoded memories via this protocol are more…
Molecular dynamics simulations are used to study the behavior of closely-fitting spherical and ellipsoidal particles moving through a fluid-filled cylinder at nanometer scales. The particle, the cylinder wall and the fluid solvent are all…
Under many conditions, biomolecules and nanoparticles associate by means of attractive bonds, due to hydrophobic attraction. Extracting the microscopic association or dissociation rates from experimental data is complicated by the…