Related papers: A Continuum Poisson-Boltzmann Model for Membrane C…
Potassium ion channels are critical components of biology. They conduct potassium ions across the cell membrane with remarkable speed and selectivity. Understanding how they do this is crucially important for applications in neuroscience,…
The Boltzmann distribution of a protein provides a roadmap to all of its functional states. Normalizing flows are a promising tool for modeling this distribution, but current methods are intractable for typical pharmacological targets; they…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
An accurate description of the structure and dynamics of interfacial water is essential for phospholipid membranes, since it determines their function and their interaction with other molecules. Here we consider water confined in stacked…
Immersed boundary methods are extensively used for simulations of dynamic solid objects interacting with fluids due to their computational efficiency and modelling flexibility compared to body-fitted grid methods. However, thin geometries,…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
We have developed a molecular mean-field theory -- fourth-order Poisson-Nernst-Planck-Bikerman theory -- for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
In this paper, we propose a computational framework,which is based on a domain decomposition technique, to employ both finite element method (which is a popular continuum modeling approach) and lattice Boltzmann method (which is a popular…
Morphological change of bilayer membrane in vivo is not a spontaneous procedure but modulated by various types of proteins in general. Most of these modulations are associated with the localization of related proteins in the crowded lipid…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
We consider the hydrodynamics of lipid bilayers containing transmembrane proteins of arbitrary shape. This biologically-motivated problem is relevant to the cell membrane, whose fluctuating dynamics play a key role in phenomena ranging from…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if those protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an…
Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. The formation of plasma membrane tubes can be due to…