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Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the…
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
Electrostatic interactions provide a convenient way to modulate interactions between nanoparticles, colloids, and biomolecules because they can be adjusted by the solution pH or salt concentration. While the presence of salt provides an…
Nanoparticles (NPs) in contact with biological fluid adsorb biomolecules into a corona. This corona comprises proteins that strongly bind to the NP (hard corona) and loosely bound proteins (soft corona) that dynamically exchange with the…
During our previous modeling using all-atom molecular dynamics, we have identified several foldamers whose nanoscale behavior resembles that of classic bistable machines, namely the Euler archs and Duffing oscillators. However, time…
We study the collective behavior of inclusions inducing local anisotropic curvatures in a flexible fluid membrane. The N-body interaction energy for general anisotropic inclusions is calculated explicitly, including multi-body interactions.…
We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…
We describe a simple coarse-grained model which is suited to study lipid layers and their phase transitions. Lipids are modeled by short semiflexible chains of beads with a solvophilic head and a solvophobic tail component. They are forced…
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing…
The dipolar interaction is known to substantially affect the properties of magnetic nanoparticles. This is particularly important when the particles are kept in a fluid suspension or packed inside nano-carriers. In addition to its usual…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
We study the potential of mean force (PMF) between atomistic silica and gold nanoparticles in the vacuum by using molecular dynamics simulations. Such an investigation is devised in order to fully characterize the effective interactions…
The reconfiguration of soft, deformable particles upon adsorption at the interface between two fluids underpins many aspects of their dynamics and interactions, ultimately controlling the macroscopic properties of particle monolayers of…
Manipulation of metal nanoparticles using atomic force microscope is a promising new technique for probing tribological properties at the nanoscale. In spite of some advancements in experimental investigations, there is no unambiguous…
The theory of elastic interaction of micron size axially symmetric colloidal particles immersed into confined nematic liquid crystal has been proposed. General formulas are obtained for the self energy of one colloidal particle and…
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…
We perform computational investigations of electrolyte-mediated interactions of charged colloidal particles confined within nanochannels. We investigate the role of discrete ion effects, valence, and electrolyte strength on colloid-wall…
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…