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Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
Molecular dynamics simulations are used to show that strong magnetization significantly increases the space and time scales associated with interparticle correlations. The physical mechanism responsible is a channeling effect whereby…
Brillouin microscopy measures compressibility, but is being increasingly used to assess stiffness of cells and tissues. Using hydrogels with tunable properties, we demonstrate that Brillouin microscopy is insensitive to stiffness of…
A tight binding model for scanning tunneling microscopy images of a molecule adsorbed on a metal surface is described. The model is similar in spirit to that used to analyze conduction along molecular wires connecting two metal leads and…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
The lack of a simple operable method for longitudinal dynamic self-assembly of particles in a microchannel is one of the main problems in applying this technology to a wide range of researches, such as biomedical engineering, material…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Dense suspensions are non-Newtonian fluids which exhibit strong shear thickening and normal stress differences. Using numerical simulation of extensional and shear flows, we investigate how rheological properties are determined by the…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
The tasks of identifying separation structures and clusters in flow data are fundamental to flow visualization. Significant work has been devoted to these tasks in flow represented by vector fields, but there are unique challenges in…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Complex fluids such as emulsions, colloidal gels, polymer or surfactant solutions are all characterized by the existence of a "microstructure" which may couple to an external flow on timescales that are easily probed in experiments. Such a…
The mixing of an impurity into a flowing fluid is an important process in many areas of science, including geophysical processes, chemical reactors, and microfluidic devices. In some cases, for example periodic flows, the concepts of…
We investigate the morphology and energetics of a self-associating model cationic surfactant in water using coarse-grained molecular dynamics simulations. We develop an algorithm to track micelles contours and quantify various…
In this work, we investigate the dynamics of the number density fluctuations of a dilute suspension of active particles in a linear viscoelastic fluid. We propose a model for the frequency-dependent diffusion coefficient of the active…
Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
The effect of non-Newtonian rheology, manifested through a viscoelastic linearized Maxwell model, on the time-dependent non-equilibrium concentration fluctuations due to free diffusion as well as thermal diffusion of a species is analyzed…
We study the scale dependence of effective diffusion of fluid tracers, specifically, its dependence on the P\'{e}clet number, a dimensionless parameter of the ratio between advection and molecular diffusion. Here, we address the case that…
Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…