Related papers: A Continuum Poisson-Boltzmann Model for Membrane C…
Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…
We give an explicit formula for the membrane potential of cells in terms of the intracellular and extracellular ionic concentrations, and derive equations for the ionic currents that flow through channels, exchangers and electrogenic pumps.…
From the perspective of physical properties, the cell membrane is an exotic two-dimensional material that has a dual nature: it exhibits characteristics of fluids, i.e., lipid molecules show lateral diffusion, while also demonstrating…
The Fluid Mosaic Model by Singer & Nicolson proposes that biological membranes consist of a fluid lipid layer into which integral proteins are embedded. The lipid membrane acts as a two-dimensional liquid in which the proteins can diffuse…
Particle methods play an important role in computational fluid dynamics, but they are among the most difficult to implement and solve. The most common method is smoothed particle hydrodynamics, which is suitable for problem settings that…
With increasing water scarcity, membrane distillation technology has gained widespread attention as an innovative method for seawater desalination.However,existing studies often overlook the influence of membrane characteristics on mass…
The specific region of an antibody responsible for binding to an antigen, known as the paratope, is essential for immune recognition. Accurate identification of this small yet critical region can accelerate the development of therapeutic…
Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue…
Symmetry is closely intertwined with the function, genetics, and chemical properties of multiprotein complexes. Here, we explore the relation between structural symmetry and the ability of membrane proteins to sense and induce membrane…
The cell-model and its treatment on the Poisson-Boltzmann level are two important concepts in the theoretical description of charged macromolecules. In this brief contribution to the Proceedings of the NATO-ASI on ``Electrostatic Effects in…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
The molecular dynamics lattice gas method maps a molecular dynamics simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method by taking a Boltzmann average…
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…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
A geometrically exact membrane formulation is presented that is based on curvilinear coordinates and isogeometric finite elements, and is suitable for both solid and liquid membranes. The curvilinear coordinate system is used to describe…
Ionic microgels are soft colloidal particles, composed of crosslinked polymer networks, that ionize and swell when dispersed in a good solvent. Swelling of these permeable, compressible particles involves a balance of electrostatic,…
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition,…
Information delivery via molecular signals is abundant in nature and potentially useful for industry sensing. Many propagation channels (e.g., tissue membranes and catalyst beds) contain porous medium materials and the impact this has on…
The plasma membrane of human red blood cells consists of a lipid bilayer attached to a regular network of underlying cytoskeletal polymers. We model this system at a dynamic coarse-grained level, treating the bilayer as an elastic sheet and…
This study examines Couette-Poiseuille flow of variable viscosity within a channel that is partially filled with a porous medium. To enhance its practical relevance, we assume that the porous medium is anisotropic with permeability varying…