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In this articlewe address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the well-known velocity-extended Poisson-Nernst-Planck (vPNP) electrodiffusion model. Two extensions of the vPNP system are proposed: the velocity-extended Thermo-Hydrodynamic...
The functionality of biomolecules depends on their flexible structures, which can be characterized by their surface shapes. Tracking the deformation and comparing biomolecular shapes are essential in understanding their mechanisms. In this paper, a new spectral shape correspondence analysis method is introduced for biomolecules based on volumetric eigenfunctions. The eigenfunctions are computed from...
A quantum corrected Poisson-Nernst-Planck (QCPNP) model is proposed for simulating ionic currents through biological ion channels by taking into account both classical and quantum mechanical effects. A generalized Gummel algorithm is also presented for solving the model system. Compared with the experimental results of X-ray crystallography, it is shown that the quantum PNP model is more accurate...
The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present...
We present an efficient and reliable algorithm for determining the orientations of noisy images obtained fromprojections of a three-dimensional object. Based on the linear relationship among the common line vectors in one image plane, we construct a sparse matrix, and show that the coordinates of the common line vectors are the eigenvectors of the matrix with respect to the eigenvalue 1. The projection...
We present a method of constructing the volume meshes of the membrane-channel protein system for finite element simulation of ion channels. The membrane channel system consists of the solvent region and the membrane-protein region. Our method focuses on labeling the tetrahedra in the solvent and membrane-protein regions and collecting the interface triangles between different regions. It contains...
Differential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications...
Protein function and dynamics are closely related to its sequence and structure.However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity between proteins based on protein sequence or physical information, serves as a crucial step toward...
Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast...
In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundaryintegral operators using the fact that their eigenfunctions are the surface spherical harmonics...
It is known that the retrovirus capsids possess a fullerene-like structure. These caged polyhedral arrangements are built entirely from hexagons and exactly 12 pentagons according to the Euler theorem. Viral capsids are composed of capsid proteins, which create the hexagon and pentagon shapes by groups of six (hexamer) and five (pentamer) proteins. Different distributions of these 12 pentamers result...
For DNA molecules, topological complexity occurs exclusively as the result of knotting or linking of the polynucleotide backbone. By contrast, while a few knots and links have been found within the polypeptide backbones of some protein structures, non-planarity can also result from the connectivity between a polypeptide chain and inter- and intra-chain linking via cofactors and disulfide bonds. In...
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