Related papers: Mesoscale computational protocols for the design o…
We examine the structural and dynamic properties of confined binary hard-sphere mixtures designed to mimic realizable colloidal thin films. Using computer simulations, governed by either Newtonian or overdamped Langevin dynamics, together…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Ligand-receptor interactions are fundamental to many biological processes. For example in antibody-based immunotherapies, the dynamics of an antibody binding with its target antigen directly influence the potency and efficacy of monoclonal…
Carefully designed nanostructures can inspire new type of optomechanical interactions and allow surpassing limitations set by classical diffractive optical elements. Apart from strong near-field localization, nanostructured environment…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Accurately predicting friction in sliding interfaces that contain third body wear particles is critical for engineering applications such as sliding movement in pistons, bearings, or metal forming. We present a hierarchical multiscale…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the…
Multi-component polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures,…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large,…
We use inverse methods of statistical mechanics to explore trade-offs associated with designing interactions to stabilize self-assembled structures against changes in density or temperature. Specifically, we find isotropic,convex-repulsive…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
Inspired by adhesive bio-filamentous structure, such as bacterial pili, this work details the methods used to fabricate and characterize a surface-anchored array of thin, flexible and shape-responsive mesoscale polymer ribbons with a…
We present a mesoscale kinetic model for multicomponent flows, augmented with a short range forcing term, aimed at describing the combined effect of surface tension and near-contact interactions operating at the fluid interface level. Such…
Frictional properties of interfaces with dynamic chemical bonds have been the subject of intensive experimental investigation and modeling, as it provides important insights into the molecular origin of the empirical rate and state laws,…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We propose a model to study symmetric binary fluids, based in the mesoscopic molecular simulation technique known as multiparticle collision, where space and state variables are continuous while time is discrete. We include a repulsion rule…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
The behavior of mesoscopic particles dissolved in a dilute solution of long, flexible, and nonadsorbing polymer chains is studied by field-theoretic methods. For spherical and cylindrical particles the solvation free energy for immersing a…