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We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…
Modulating ion transport through nanoporous membranes is critical to many important chemical and biological separation processes. The corresponding transport timescales, however, are often too long to capture accurately using conventional…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
Chemically powered self-propelled colloids generate a motor force by converting locally a source of energy into directed motion, a process that has been explored both in experiments and in computational models. The use of active colloids as…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
We use a coarse-grained molecular dynamics simulation to investigate the interaction between neutral or charged nanoparticles (NPs) and a vesicle consisting of neutral and negatively charged lipids. We focus on the interaction strengths of…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
Current voltage (I-V) characteristics in proteins can be sensitive to conformational change induced by an external stimulus (photon, odour, etc.). This sensitivity can be used in medical and industrial applications besides shedding new…
We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitors. The organic electrolyte consists in 1-ethyl-3-methyl--imidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores in physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl…
Ion transport through charged nanopores is commonly interpreted in terms of electrical double layer structure, leading to the expectation of cation-selective conduction in negatively charged pores. This picture can break down for…
Cementitious materials are widely used for hazardous-waste encapsulation, yet the molecular mechanisms governing heavy-metal ion retention across different gel chemistries remain insufficiently resolved. Here, classical molecular dynamics…
In recent years, several artificial molecular motors driven and controlled by electric currents have been proposed. Similar to Brownian machines, these systems work by turning random inelastic tunneling events into a directional rotation of…
Ionic liquids constrained at interfaces or restricted in subnanometric pores are increasingly employed in modern technologies, including energy applications. Understanding the details of their behavior in these conditions is therefore…
We report a molecular dynamics (MD) simulation study of reverse osmosis desalination using nanoporous monolayer graphene passivated by SiH$_2$ and Si(OH)$_2$ functional groups. A highly accurate and detailed polarizable molecular mechanics…