Related papers: Variational Methods for Biomolecular Modeling
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
We derive an asymptotically consistent morphoelastic shell model to describe the finite deformations of biological tissues using the variational asymptotical method. Biological materials may exhibit remarkable compressibility when under…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…
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 overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
Molecular adsorption at organic/metal interfaces depends on a range of mechanisms: covalent bonds, charge transfer, Pauli repulsion and van der Waals (vdW) interactions shape the potential energy surface (PES), making it key to…
As a classical generative modeling approach, energy-based models have the natural advantage of flexibility in the form of the energy function. Recently, energy-based models have achieved great success in modeling high-dimensional data in…
We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the \textit{morphometric} calculation of $n$-body correlations. We calculate absolute free energies of local geometric…
Multiscale and multiphysics problems need novel numerical methods in order for them to be solved correctly and predictively. To that end, we develop a wavelet based technique to solve a coupled system of nonlinear partial differential…
This article offers a new perspective for the mechanics of solids using moving Cartan's frame, specifically discussing a mixed variational principle in non-linear elasticity. We treat quantities defined on the co-tangent bundles of…
We present a projection-based numerical integration technique to deal with embedded interface in finite element (FE) framework. The element cut by an embedded interface is denoted as a cut cell. We recognize elemental matrices of a cut cell…
We introduce an optimisation method for variational quantum algorithms and experimentally demonstrate a 100-fold improvement in efficiency compared to naive implementations. The effectiveness of our approach is shown by obtaining…
In many interfacial flow systems, variations of surface properties lead to novel and interesting behaviors. In this work a three-dimensional model of flow dynamics for multicomponent vesicles is presented. The surface composition is modeled…
Key properties of physical systems can be described by the eigenvalues of matrices that represent the system. Computational algorithms that determine the eigenvalues of these matrices exist, but they generally suffer from a loss of…
Variational inference in probabilistic graphical models aims to approximate fundamental quantities such as marginal distributions and the partition function. Popular approaches are the Bethe approximation, tree-reweighted, and other types…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
The use of energy functionals based on density as the basic variable is advocated for ab initio molecular dynamics. It is demonstrated that the constraint of positivity of density can be incorporated easily by using square root density for…
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…