Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Global Energy Matching Method for Atomistic-to-Continuum Modeling of Self-Assembling Biopolymer Aggregates

This paper studies mathematical models of biopolymer supramolecular aggregates that are formed by the self-assembly of single monomers. We develop a new multiscale numerical approach to model the structural properties of such aggregates. This theoretical approach establishes micro-macro relations between the geometrical and mechanical properties of the monomers and supramolecular aggregates. Most atomistic-to-continuum methods are constrained by a crystalline order or a periodic setting and therefore cannot be directly applied to modeling of soft matter. By contrast, the energy matching method developed in this paper does not require crystalline order and, therefore, can be applied to general microstructures with strongly variable spatial correlations. In this paper we use this method to compute the shape and the bending stiffness of their supramolecular aggregates from known chiral and amphiphilic properties of the short chain peptide monomers. Numerical implementation of our approach demonstrates consistency with results obtained by molecular dynamics simulations

AROMA: Automatic Generation of Radio Maps for Localization Systems

WLAN localization has become an active research field recently. Due to the wide WLAN deployment, WLAN localization provides ubiquitous coverage and adds to the value of the wireless network by providing the location of its users without using any additional hardware. However, WLAN localization systems usually require constructing a radio map, which is a major barrier of WLAN localization systems' deployment. The radio map stores information about the signal strength from different signal strength streams at selected locations in the site of interest. Typical construction of a radio map involves measurements and calibrations making it a tedious and time-consuming operation. In this paper, we present the AROMA system that automatically constructs accurate active and passive radio maps for both device-based and device-free WLAN localization systems. AROMA has three main goals: high accuracy, low computational requirements, and minimum user overhead. To achieve high accuracy, AROMA uses 3D ray tracing enhanced with the uniform theory of diffraction (UTD) to model the electric field behavior and the human shadowing effect. AROMA also automates a number of routine tasks, such as importing building models and automatic sampling of the area of interest, to reduce the user's overhead. Finally, AROMA uses a number of optimization techniques to reduce the computational requirements. We present our system architecture and describe the details of its different components that allow AROMA to achieve its goals. We evaluate AROMA in two different testbeds. Our experiments show that the predicted signal strength differs from the measurements by a maximum average absolute error of 3.18 dBm achieving a maximum localization error of 2.44m for both the device-based and device-free cases.Comment: 14 pages, 17 figure

Application of the level-set method to the implicit solvation of nonpolar molecules

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}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system

Gravitational perturbations of Schwarzschild spacetime at null infinity and the hyperboloidal initial value problem

We study gravitational perturbations of Schwarzschild spacetime by solving a hyperboloidal initial value problem for the Bardeen-Press equation. Compactification along hyperboloidal surfaces in a scri-fixing gauge allows us to have access to the gravitational waveform at null infinity in a general setup. We argue that this hyperboloidal approach leads to a more accurate and efficient calculation of the radiation signal than the common approach where a timelike outer boundary is introduced. The method can be generalized to study perturbations of Kerr spacetime using the Teukolsky equation.Comment: 14 pages, 9 figure