Computational Physics
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
By using the quantum Ising chain as a test bed and treating the spin polarization along the external transverse field as the "generalized density", we examine the performance of different levels of density functional approximations parallel…
The JOREK extended magneto-hydrodynamic (MHD) code is a widely used simulation code for studying the non-linear dynamics of large-scale instabilities in divertor tokamak plasmas. Due to the large scale-separation intrinsic to these…
The invariant distribution, which is characterized by the stationary Fokker-Planck equation, is an important object in the study of randomly perturbed dynamical systems. Traditional numerical methods for computing the invariant distribution…
Stochastic dynamical systems with continuous symmetries arise commonly in nature and often give rise to coherent spatio-temporal patterns. However, because of their random locations, these patterns are not well captured by current order…
In this paper, a methodology for modelling two-phase flows based on a conservative level set method in the framework of finite volume method is presented. The novelty of the interface capturing method used here lies on the advection of…
Understanding the thermal vibrations and thermal transport in amorphous materials is an important but long-standing issue in several theoretical and practical fields. Using direct molecular dynamic simulations, we demonstrate that the…
Excitonic effects in 1D semiconductors can be qualitatively different from those in higher dimensions. In particular, the Sommerfeld factor, the ratio of the above-band-edge excitonic continuum absorption to free electron-hole pair…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
A "two-dimensional ballistic deposition" (2D-BD) code has been developed to study the geometric effects in ballistic deposition of thin-film growth. Circular discs are used as depositing specie to understand the shadowing effects during the…
Inverse problems exist in many domains such as phase imaging, image processing, and computer vision. These problems are often solved with application-specific algorithms, even though their nature remains the same: mapping input image(s) to…
The Ising machine is an unconventional computing architecture that can be used to solve NP-hard combinatorial optimization problems more efficiently than traditional von Neumann architectures. Fast, compact oscillator networks which provide…
Predictive simulations of complex systems are essential for applications ranging from weather forecasting to drug design. The veracity of these predictions hinges on their capacity to capture the effective system dynamics. Massively…
We present rotating periodic boundary conditions (PBCs) for the simulation of nonequilibrium molecular dynamics (NEMD) under uniaxial stretching flow (USF) or biaxial stretching flow (BSF). Such nonequilibrium flows need specialized PBCs…
Properties of inorganic-organic interfaces, such as their interface dipole, strongly depend on the structural arrangements of the organic molecules. A prime example is tetracyanoethylene (TCNE) on Cu(111), which shows two different phases…
A fully conservative sharp-interface method is developed for multiphase flows with phase change. The coupling between two phases is implemented via introducing the interfacial fluxes, which are obtained by solving a general Riemann problem…
Three-dimensional electron tomography is used to understand the structure and properties of samples in chemistry, materials science, geoscience, and biology. With the recent development of high-resolution detectors and algorithms that can…
Solving the wave equation numerically constitutes the majority of the computational cost for applications like seismic imaging and full waveform inversion. An alternative approach is to solve the frequency domain Helmholtz equation, since…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram Analysis Method (WHAM) which is an iterative post-processing…