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The solution of partial differential equations (PDEs) on complex domains often presents a significant computational challenge by requiring the generation of fitted meshes. The Diffuse Domain Method (DDM) is an alternative which reformulates…
The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a…
Atomic diffusion affects the properties of various engineering materials, which predominantly occur in the polycrystalline state. A rigorous description of polycrystalline diffusion must therefore account for crystallographic defects,…
The immersed boundary (IB) method is a general mathematical framework for studying problems involving fluid-structure interactions in which an elastic structure is immersed in a viscous incompressible fluid. In the IB formulation, the fluid…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Control Barrier Functions (CBFs) have been demonstrated to be a powerful tool for safety-critical controller design for nonlinear systems. Existing design paradigms do not address the gap between theory (controller design with continuous…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and…
In this paper, the Immersed Boundary Method (IBM) proposed by Pinelli is implemented for finite volume approximations of incompressible Navier-Stokes equations solutions in the open source toolbox OpenFOAM version 2.2. Solid obstacles are…
Molecule-metal interfaces have a broad range of applications in nanoscale materials science. Accurate characterization of their electronic structures from first-principles is key in understanding material and device properties. The GW…
This study presents an advanced sharp-interface immersed boundary method (IBM) integrated with the blastFOAM library on the OpenFOAM platform for high-speed compressible flow simulations. The developed solver extends the existing IBM…
The aim of this paper is to propose a novel methodology to deal with micro-structural boundary conditions for the analysis of granular materials. The response of the granular assembly is modelled through the discrete element method (DEM),…
This article solves two major tasks that frequently arise in the theory of electron collisions with a target molecular cation. First, it extends the energy-dependent frame transformation treatment(EDFT), which is needed to map fixed-nuclei…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
In this work, we investigate the diffusive optical tomography (DOT) problem in the case that limited boundary measurements are available. Motivated by the direct sampling method (DSM), we develop a deep direct sampling method (DDSM) to…
Recent studies suggest that cosolute mixtures may exert significant non-additive effects upon protein stability. The corresponding liquid-vapor interfaces may provide useful insight into these non-additive effects. Accordingly, in this work…