Related papers: Plumbing Analog of Molecular Computation
Symmetry breaking is essential for biological microswimmers to achieve locomotion in viscous environments. Such asymmetry in the swimming mechanism enables the generation of directional forces that overcome fluid resistance, leading to…
We describe an example of a structurally stable heteroclinic network for which nearby orbits exhibit irregular but sustained switching between the various sub-cycles in the network. The mechanism for switching is the presence of spiralling…
Solid/liquid interfaces control various processes of technological relevance in the process industry and many fundamental physicochemical phenomena. This work examines the link between the atomistic description of mass transfer at…
We discuss electronic properties and their evolution for the linear chain of $H_2$ molecules in the presence of a uniform external force $f$ acting along the chain. The system is described by an extended Hubbard model within a fully…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
Capturing the dynamics of active particles, i.e., small self-propelled agents that both deform and are deformed by a fluid in which they move is a formidable problem as it requires coupling fine scale hydrodynamics with large scale…
Machine learning models for the potential energy of multi-atomic systems, such as the deep potential (DP) model, make possible molecular simulations with the accuracy of quantum mechanical density functional theory, at a cost only…
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
One of the key choices for numerical models of geophysical fluids is how parametrisations of physical processes interact with the numerical methods that handle the resolved flow, known in the atmospheric community as the dynamical core. As…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…