Related papers: Mesoscale computational protocols for the design o…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
The efficacy of drug treatments depends on how tightly small molecules bind to their target proteins. The rapid and accurate quantification of the strength of these interactions (as measured by binding affinity) is a grand challenge of…
Nature is remarkably adept at using interfaces to build structures, encapsulate reagents, and regulate biological processes. Inspired by Nature, we describe flexible polymer-based ribbons, termed "mesoscale polymers" (MSPs), to modulate…
Characterizing the connection between material design decisions/parameters and their effective properties allows for accelerated materials development and optimization. We present a global sensitivity analysis of woven composite…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
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…
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from…
The properties of constrained fluids have increasingly gained relevance for applications ranging from materials to biology. In this work, we propose a multiscale model using twin neural networks to investigate the properties of a fluid…
We design dipolar quantum many-body Hamiltonians that will facilitate the realization of exotic quantum phases under current experimental conditions achieved for polar molecules. The main idea is to modulate both single-body potential…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
Recent years have seen dramatic progress in the development of techniques for measuring the activity and connectivity of large populations of neurons in the brain. However, as these techniques grow ever more powerful---allowing us to even…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell $-$ functions that are inherently connected to their physical properties. A remarkable aspect of such condensates is that…
Ligand coated nanoparticles are complex objects consisting of a metallic or semiconductor core with organic ligands grafted on their surface. These organic ligands provide stability to a nanoparticle suspension. In solutions, the effective…