Related papers: The minimal molecular surface
Magnetic particle spectroscopy (MPS) is a technology that derives from magnetic particle imaging (MPI) and thrives as a standalone platform for many biological and biomedical applications, benefiting from the facile preparation and chemical…
The molecular structure of moving contact lines (MCLs) and the emergence of a corresponding macroscopic dissipation have made the MCL a paradigm of fluid dynamics. Through novel averaging techniques that remove capillary waves smearing we…
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104},…
MSS is an algorithm to determine the radii and positions of spheres that fill a given volume. In the context of granular materials, MSS is a particle generator for DEM simulations of complex-shaped particles. Here, each particle of a given…
We present a framework for solving partial different equations on evolving surfaces. Based on the grid-based particle method (GBPM) [18], the method can naturally resample the surface even under large deformation from the motion law. We…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical…
Mass spectrometry (MS) stands as a cornerstone analytical technique for molecular identification, yet de novo structure elucidation from spectra remains challenging due to the combinatorial complexity of chemical space and the inherent…
Non-negative matrix factorization (NMF) is a natural model of admixture and is widely used in science and engineering. A plethora of algorithms have been developed to tackle NMF, but due to the non-convex nature of the problem, there is…
This paper addresses the problem of mapping high-dimensional data to a low-dimensional space, in the presence of other known features. This problem is ubiquitous in science and engineering as there are often controllable/measurable features…
The structure of the MSSM is reviewed. We first motivate the particle content of the theory by examining the quantum numbers of the known standard model particles and by the requirement of anomaly cancellation. Once the particle content is…
A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
We investigate the existence of minimal hypersurfaces in $\mathbb{S}^{n+1}$ that are generated by the isoparametric foliation of a subsphere $\mathbb{S}^n$. By considering a generalized rotational ansatz formed by the union of homothetic…
This study focuses on solving the numerical challenges of imposing absorbing boundary conditions for dynamic simulations in the material point method (MPM). To attenuate elastic waves leaving the computational domain, the current work…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…