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1. Asymmetric membrane “sticky tape” enables simultaneous relaxation of area and curvature in simulation

   https://doi.org/10.1063/5.0189771  

   Foley, Samuel L; Deserno, Markus (February 2024, The Journal of Chemical Physics)

   Biological lipid membranes are generally asymmetric, not only with respect to the composition of the two membrane leaflets but also with respect to the state of mechanical stress on the two sides. Computer simulations of such asymmetric membranes pose unique challenges with respect to the choice of boundary conditions and ensemble in which such simulations are to be carried out. Here, we demonstrate an alternative to the usual choice of fully periodic boundary conditions: The membrane is only periodic in one direction, with free edges running parallel to the single direction of periodicity. In order to maintain bilayer asymmetry under these conditions, nanoscale “sticky tapes” are adhered to the membrane edges in order to prevent lipid flip-flop across the otherwise open edge. In such semi-periodic simulations, the bilayer is free to choose both its area and mean curvature, allowing for minimization of the bilayer elastic free energy. We implement these principles in a highly coarse-grained model and show how even the simplest examples of such simulations can reveal useful membrane elastic properties, such as the location of the monolayer neutral surface. 

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2. Computational Fluid Dynamics Modeling of Material Deposition in Pneumatic Micro-Extrusion Additive Manufacturing

   O’Malley, Ethan; Salary, Roozbeh “Ross” (July 2025, American Society of Mechanical Engineers (ASME) - International Mechanical Engineering Congress and Exposition (IMECE 2025))

   Pneumatic micro-extrusion (PME) presents inherent challenges in achieving precise control over material deposition due to the small scale and high viscosity of the material flow. Traditional experimental methods often fall short in capturing the complex mechanisms, interactions, and dynamics governing material transport and deposition in PME, highlighting the necessity for advanced computational approaches to unveil these intricate physical phenomena. The primary objective of this study is to develop a robust computational framework for simulating material transport and deposition in PME, offering detailed insights into the fluid dynamics, flow complexities, and deposition characteristics intrinsic to the PME process. This involves systematically investigating the influence of key process parameters, such as material properties, print speed, and flow pressure, on deposition dynamics. Three-dimensional (3D) computational fluid dynamics (CFD) modeling was employed using ANSYS Fluent, with boundary conditions defined to replicate pneumatic extrusion on a moving substrate. The CFD simulations captured three distinct deposition regimes: (i) under-extrusion, (ii) normal extrusion, and (iii) over-extrusion. Results show that decreasing print speed at constant inlet velocity produced over-extrusion, with increased bead height and width due to material overflow. At normal extrusion, bead geometry remained stable, while under-extrusion reduced bead width and ultimately led to discontinuities when flow stresses exceeded cohesive strength. Notably, bead width decreased significantly between 10 mm/s and 15 mm/s, but showed little difference between 15 mm/s and 20 mm/s. Instead, the higher speed produced discontinuities consistent with experimental observations. Centerline velocity profiles revealed that the flow inside the cartridge was very slow at approximately 0.058 mm/s, whereas the velocity increased sharply within the nozzle throat, reaching nearly 12.88 mm/s. These predictions were further supported by validation experiments, where the measured nozzle velocity of 12.95 mm/s closely matched the CFD-simulated value of 12.88 mm/s, demonstrating strong agreement between simulation and experiment. Additionally, pressure decreased slightly with increasing print speed due to reduced backflow, while nozzle velocity and wall shear stress remained unchanged under fixed inlet velocity conditions. Overall, the outcomes of this study are expected to inform parameter optimization strategies and enhance PME process efficiency, providing critical insights into how variations in PME process dynamics influence print morphology and quality, advancing the path toward optimized fabrication of scaffolds for tissue engineering applications. 

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3. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics

   https://doi.org/10.1063/5.0219851  

   Pederson, John P; McDaniel, Jesse G (July 2024, The Journal of Chemical Physics)

   PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule’s electron density. 

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4. Estimating the interfacial permeability for flow into a poroelastic medium

   https://doi.org/10.1039/D4SM00476K  

   Xu, Zelai; Yue, Pengtao; Feng, James J (June 2024, Soft Matter)

   Boundary conditions between a porous solid and a fluid has been a long-standing problem in modeling porous media. For deformable poroelastic materials such as hydrogels, the question is further complicated by the elastic stress from the solid network. Recently, an interfacial permeability condition has been developed from the principle of positive energy dissipation on the hydrogel–fluid interface. Although this boundary condition has been used in flow computations and yielded reasonable predictions, it contains an interfacial permeability g as a phenomenological parameter. In this work, we use porescale models of flow into a periodic array of solid cylinders or parallel holes to determine g as a function of the pore size and porosity. This provides a means to evaluate the interfacial permeability for a wide range of poroelastic materials, including hydrogels, foams and biological tissues, to enable realistic flow simulations. 

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5. Computing hydrodynamic interactions in confined doubly periodic geometries in linear time

   https://doi.org/10.1063/5.0141371  

   Hashemi, Aref; Peláez, Raúl P.; Natesh, Sachin; Sprinkle, Brennan; Maxian, Ondrej; Gan, Zecheng; Donev, Aleksandar (April 2023, The Journal of Chemical Physics)

   We develop a linearly scaling variant of the force coupling method [K. Yeo and M. R. Maxey, J. Fluid Mech. 649, 205–231 (2010)] for computing hydrodynamic interactions among particles confined to a doubly periodic geometry with either a single bottom wall or two walls (slit channel) in the aperiodic direction. Our spectrally accurate Stokes solver uses the fast Fourier transform in the periodic xy plane and Chebyshev polynomials in the aperiodic z direction normal to the wall(s). We decompose the problem into two problems. The first is a doubly periodic subproblem in the presence of particles (source terms) with free-space boundary conditions in the z direction, which we solve by borrowing ideas from a recent method for rapid evaluation of electrostatic interactions in doubly periodic geometries [Maxian et al., J. Chem. Phys. 154, 204107 (2021)]. The second is a correction subproblem to impose the boundary conditions on the wall(s). Instead of the traditional Gaussian kernel, we use the exponential of a semicircle kernel to model the source terms (body force) due to the presence of particles and provide optimum values for the kernel parameters that ensure a given hydrodynamic radius with at least two digits of accuracy and rotational and translational invariance. The computation time of our solver, which is implemented in graphical processing units, scales linearly with the number of particles, and allows computations with about a million particles in less than a second for a sedimented layer of colloidal microrollers. We find that in a slit channel, a driven dense suspension of microrollers maintains the same two-layer structure as above a single wall, but moves at a substantially lower collective speed due to increased confinement. 

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