Related papers: Mesoscale computational protocols for the design o…
We study and predict the interfacial tension, solubility parameters and Flory-Huggins parameters of binary mixtures as functions of pressure and temperature, using multiscale numerical simulation. A mesoscopic approach is proposed for…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Over the last few decades, nonlinear optics has become significantly more nonlinear, traversing nearly a billionfold improvement in energy efficiency, with ultrafast nonlinear nanophotonics in particular emerging as a frontier for combining…
Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. In this work, we introduce a new,…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
Understanding the binding dynamics of liquid molecules is of fundamental importance in physical and life sciences. However, nanoscale fast dynamics pose great challenges for experimental characterization. Conventionally, the binding…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
We consider two minimal mathematical models for cancer dynamics and self-adaptation. We aim to capture the interplay between the rapid progression of cancer growth and the possibility to leverage and enhance self-adaptive defense mechanisms…
Material properties are fundamentally dictated by multiscale phenomena, which often reach mesoscale in size. The {\mu}m mesoscale is also the size which can be observed directly under an optical microscope, bridging the atomistic…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Auxiliary nanostructures introduce additional flexibility into optomechanical manipulation schemes. Metamaterials and metasurfaces capable to control electromagnetic interactions at the near-field regions are especially beneficial for…
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…
From self-assembly and protein folding to combinatorial metamaterials, a key challenge in material design is finding the right combination of interacting building blocks that yield targeted properties. Such structures are fiendishly…
Single molecule probes are widely used to characterize dynamic heterogeneity in glass forming liquids, but interpreting probe dynamics remains challenging because the measured response depends on how the probe couples to its host…