Physics - Computational Physics Publications (50)

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Physics - Computational Physics Publications

Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic or near-atomic resolution. However, applications are so far mainly limited to radiation-hard samples because the required doses are too high for imaging biological samples at high resolution. We propose the use of non-convex, Bayesian optimization to overcome this problem and reduce the dose required for successful reconstruction by two orders of magnitude compared to previous experiments. Read More


MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. Read More


In this article, a few problems related to multiscale modelling of magnetic materials at finite temperatures and possible ways of solving these problems are discussed. The discussion is mainly centred around two established multiscale concepts: the partitioned domain and the upscaling-based methodologies. The major challenge for both multiscale methods is to capture the correct value of magnetisation length accurately, which is affected by a random temperature-dependent force. Read More


Sand fences are widely applied to prevent soil erosion by wind in areas affected by desertification. Sand fences also provide a way to reduce the emission rate of dust particles, which is triggered mainly by the impacts of wind-blown sand grains onto the soil and affects the Earth's climate. Many different types of fence have been designed and their effects on the sediment transport dynamics studied since many years. Read More


An extended atomistic spin model allowing for studies of the finite temperature magnetic properties of alloys is proposed. The model is obtained by extending the Heisenberg Hamiltonian via a parameterization from a first principles basis, interpolating from both the low temperature ferromagnetic and the high temperature paramagnetic reference states. This allows us to treat magnetic systems with varying degree of itinerant character within the model. Read More


The direct numerical simulation of particulate systems offers a unique approach to study the dynamics of fluid-solid suspensions by fully resolving the submerged particles and without introducing empirical models. For the lattice Boltzmann method, different variants exist to incorporate the fluid-particle interaction into the simulation. This paper provides a detailed and systematic comparison of two different methods, namely the momentum exchange method and the partially saturated cells method by Noble and Torczynski. Read More


Attosecond x-ray pulses offer unprecedented opportunities for probing and triggering new types of ultrafast motion. At the same time, pulse characterization of x-rays presents new challenges that do not exist in the UV regime. Inner-shell ionization is the dominant ionization mechanism for x-rays and it is followed by secondary processes like fluorescence, Auger decay, and shake-up. Read More


The Finite Difference (FD) and the Spectral Boundary Integral (SBI) methods have been used extensively to model spontaneously propagating shear cracks in a variety of engineering and geophysical applications. In this paper, we propose a new modeling approach, in which these two methods are combined through consistent exchange of boundary tractions and displacements. Benefiting from the flexibility of FD and the efficiency of spectral boundary integral (SBI) methods, the proposed hybrid scheme will solve a wide range of problems in a computationally efficient way. Read More


Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher order accurate relativistic PIC algorithm in one spatial dimension which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher order interpolation functions to achieve a spatially higher order accurate algorithm (up to 5th order). Read More


We develop a robust method for simulating vesicle suspensions in a two-dimensional Stokesian fluid at low discretization resolutions. Vesicle suspensions model biological systems such as microcirculation, where the blood flow is dictated by red blood cells. Vesicle flows are characterized by rich and complex dynamics of vesicles due to their large deformations and nonlinear elastic properties. Read More


We study the influence of external pressure on the electronic and magnetic structure of EuMnO3 from first-principles calculations. We find a pressure-induced insulator-metal transition at which the magnetic order changes from A-type antiferromagnetic to ferromagnetic with a strong interplay with Jahn-Teller distortions. In addition, we find that the non-centrosymmetric E*-type antiferromagnetic order can become nearly degenerate with the ferromagnetic ground state in the high-pressure metallic state. Read More


We develop and analyze quadrature blending schemes that minimize the dispersion error of isogeometric analysis up to polynomial order seven with maximum continuity in the span ($C^{p-1}$). The schemes yield two extra orders of convergence (superconvergence) on the eigenvalue errors, while the eigenfunction errors are of optimal convergence order. Both dispersion and spectrum analysis are unified in the form of a Taylor expansion for eigenvalue errors. Read More


In the upscaling from pore- to continuum (Darcy) scale, reaction and deposition phenomena at the solid-liquid interface of a porous medium have to be represented by macroscopic reaction source terms. The effective rates can be computed, in the case of periodic media, from three-dimensional microscopic simulations of the periodic cell. Several computational and semi-analytical models have been studied in the field of colloid filtration to describe this problem. Read More


This paper describes a lattice Boltzmann-based binary fluid model for inkjet printing. In this model, a time-dependent driving force is applied to actuate the droplet ejection. As a result, the actuation can be accurately controlled by adjusting the intensity and duration of the positive and negative forces, as well as the idle time. Read More


Contact angle is an essential characteristic in wetting, capillarity and moving contact line; however, although contact angle phenomena are effectively simulated, an accurate and real-time measurement for this characteristic has not been well studied in computational fluid dynamics, especially in dynamic environments. Here, we design a geometry-based mesoscopic scheme to onthesport measure the contact angle in the lattice Boltzmann method. The computational results without gravity effect are in excellent agreement with the benchmarks from the spherical cap method. Read More


The Hierarchical Schur Complement method (HSC), and the HSC-extension, have significantly accelerated the evaluation of the retarded Green's function, particularly the lesser Green's function, for two-dimensional nanoscale devices. In this work, the HSC-extension is applied to determine the solution of non-equilibrium Green's functions (NEGF) on three-dimensional nanoscale devices. The operation count for the HSC-extension is analyzed for a cuboid device. Read More


The mathematical foundation of the so-called extended coupled-cluster method for the solution of the many-fermion Schr\"odinger equation is here developed. We prove an existence and uniqueness result, both in the full infinite-dimensional amplitude space as well as for discretized versions of it. The extended coupled-cluster method is formulated as a critical point of an energy function using a generalization of the Rayleigh-Ritz principle: the bivariational principle. Read More


An electrified visco-capillary jet shows different dynamic behavior, such as cone forming, breakage into droplets, whipping and coiling, depending on the considered parameter regime. The whipping instability that is of fundamental importance for electrospinning has been approached by means of stability analysis in previous papers. In this work we alternatively propose a model framework in which the instability can be computed straightforwardly as the stable stationary solution of an asymptotic Cosserat rod description. Read More


This paper describes an efficient algorithm for computing steady two-dimensional surface gravity wave in irrotational motion. The algorithm complexity is O(N log N), N being the number of Fourier modes. The algorithm allows the arbitrary precision computation of waves in arbitrary depth, i. Read More


Motivated by the recently proposed parallel orbital-updating approach in real space method, we propose a parallel orbital-updating based plane-wave basis method for electronic structure calculations, for solving the corresponding eigenvalue problems. In addition, we propose two new modified parallel orbital-updating methods. Compared to the traditional plane-wave methods, our methods allow for two-level parallelization, which is particularly interesting for large scale parallelization. Read More


We introduce a hybrid approach to applying the density matrix renormalization group (DMRG) to continuous systems, combining a grid approximation along one direction with a finite Gaussian basis set along the remaining two directions. This approach is especially useful for chain-like molecules, where the grid is used in the long direction, and we demonstrate the approach with results for hydrogen chains. The computational time for this system scales approximately linearly with the length of the chain, as we demonstrate with minimal basis set calculations with up to 1000 atoms, which are near-exact within the basis. Read More


The attainability of modification of the apparent magnetic anisotropy in (III,Mn)V ferromagnetic semiconductors is probed by means of the finite-elements-based modelling. The most representative case of (Ga,Mn)As and its in-plane uniaxial anisotropy is investigated. The hysteresis loops of the continuous films of a ferromagnetic semiconductor as well as films structured with the elliptic antidots are modelled for various eccentricity, orientation, and separation of the anti dots. Read More


In the present paper the behavior of a single artificial microswimmer is addressed, namely an active droplet moving by Marangoni flow. The non-uniform surface tension distribution underlying the propulsion mechanism of the droplet, is generated by a non-uniform distribution of surfactant on its surface. We provide a numerical treatment for the main factors playing a role in real systems, such as advection, diffusion and the presence of chemical species with different behaviors. Read More


The second-order extended stability Factorized Runge-Kutta-Chebyshev (FRKC2) class of explicit schemes for the integration of large systems of PDEs with diffusive terms is presented. FRKC2 schemes are straightforward to implement through ordered sequences of forward Euler steps with complex stepsizes, and easily parallelised for large scale problems on distributed architectures. Preserving 7 digits for accuracy at 16 digit precision, the schemes are theoretically capable of maintaining internal stability at acceleration factors in excess of 6000 with respect to standard explicit Runge-Kutta methods. Read More


Accurate prediction of the electronic and hydrogen storage properties of linear carbon chains (Cn) and Li-terminated linear carbon chains (Li2Cn), with n carbon atoms (n = 5 - 10), has been very challenging for traditional electronic structure methods, due to the presence of strong static correlation effects. To meet the challenge, we study these properties using our newly developed thermally-assisted-occupation density functional theory (TAO-DFT), a very efficient electronic structure method for the study of large systems with strong static correlation effects. Owing to the alteration of the reactivity of Cn and Li2Cn with n, odd-even oscillations in their electronic properties are found. Read More


FeRh is a showcase for caloric materials genome, transforming upon heating from the type-2 antiferromagnet (AFM) to a ferromagnet (FM). FeRh AFM (but not FM) cubic B2 lattice is unstable at ambient pressure. We describe the stable orthorhombic AFM FeRh structure at low temperature T. Read More


Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. Read More


In this article, two novel numerical methods have been developed for simulating fluid/porous particle interactions in three-dimensional (3D) Stokes flow. The Brinkman-Debye-Bueche model is adopted for the fluid flow inside the porous particle, being coupled with the Stokes equations for the fluid flow outside the particle. The rotating motion of a porous ball and the interaction of two porous balls in bounded shear flows have been studied by these two new methods. Read More


We investigate the defect structures forming around two nanoparticles in a Gay-Berne nematic liquid crystal using molecular simulations. For small separations, disclinations entangle both particles forming the figure of eight, the figure of omega and the figure of theta. These defect structures are similar in shape and occur with a comparable frequency to micron-sized particles studied in experiments. Read More


Surface force apparatus (SFA) and atomic force microscopy (AFM) can measure a force curve between a substrate and a probe in liquid. However, the force curve had not been transformed to the number density distribution of solvent molecules (colloidal particles) on the substance due to the absence of such a transform theory. Recently, we proposed and developed the transform theories for SFA and AFM. Read More


Anisotropy describes the directional dependence of a material's properties such as transport and optical response. In conventional bulk materials, anisotropy is intrinsically related to the crystal structure, and thus not tunable by the gating techniques used in modern electronics. Here we show that, in bilayer black phosphorus with an interlayer twist angle of 90{\deg}, the anisotropy of its electronic structure and optical transitions is tunable by gating. Read More


Knowledge of the topology of the electronic ground state of materials has led to deep insights to novel phenomena such as the integer quantum Hall effect and fermion-number fractionalization, as well as other properties of matter. Joining two insulators of different topological classes produces fascinating boundary states in the band gap. Another exciting recent development is the bottom-up synthesis (from molecular precursors) of graphene nanoribbons (GNRs) with atomic precision control of their edge and width. Read More


Predicting the response of a system to perturbations is a key challenge in mathematical and natural sciences. Under suitable conditions on the nature of the system, of the perturbation, and of the observables of interest, response theories allow to construct operators describing the smooth change of the invariant measure of the system of interest as a function of the small parameter controlling the intensity of the perturbation. In particular, response theories can be developed both for stochastic and chaotic deterministic dynamical systems, where in the latter case stricter conditions imposing some degree of structural stability are required. Read More


In this paper we describe a high-resolution transport formulation of the regional level-set approach for an improved prediction of the evolution of complex interface networks. The novelty of this method is twofold: (i) construction of local level sets and reconstruction of a global regional level sets, (ii) locally transporting the interface network by employing high-order spatial discretization schemes for improved representation of complex topologies. Various numerical test cases of multi-region flow problems, including triple-point advection, single vortex flow, mean curvature flow, normal driven flow and dry foam dynamics, show that the method is accurate and suitable for a wide range of complex interface-network evolutions. Read More


Understanding the mechanism of the heterojunction is an important step towards controllable and tunable interfaces for photocatalytic and photovoltaic based devices. To this aim, we propose a thorough study of a double heterostructure system consisting of two semiconductors with large band gap, namely, wurtzite ZnO and anatase TiO$_2$. We demonstrate via first-principle calculations two stable configurations of ZnO/TiO$_2$ interfaces. Read More


We adapt and extend a formulation for soluble surfactant transport in multiphase flows recently presented by Muradoglu & Tryggvason (JCP 274 (2014) 737-757) to the context of the Level Contour Reconstruction Method (Shin et al. IJNMF 60 (2009) 753-778) which is a hybrid method that combines the advantages of the Front-tracking and Level Set methods. Particularly close attention is paid to the formulation and numerical implementation of the surface gradients of surfactant concentration and surface tension. Read More


In this paper, a novel field function is presented for low-memory-cost multimaterial mesh generation and fast collision detection. In addition, a multi-body collision model with parameterized elasticity and friction is devised for modelling deterministic and realistic particle-particle interactions. The devised field function and collision model are able to effectively achieve direct simulations of fluid-solid systems with dense and irregular particles. Read More


The accurate prediction of singlet and triplet excitation energies is of significant fundamental interest and is critical for many applications. An area of intense research, most calculations of singlet and triplet energies use time-dependent density functional theory (TDDFT) in conjunction with an approximate exchange-correlation functional. In this work, we examine and critically assess an alternative method for predicting low-lying neutral excitations with similar computational cost, the ab initio Bethe-Salpeter equation (BSE) approach, and compare results against high-accuracy wavefunction-based methods. Read More


Three complementary methods have been implemented in the code Denovo that accelerate neutral particle transport calculations with methods that use leadership-class computers fully and effectively: a multigroup block (MG) Krylov solver, a Rayleigh quotient iteration (RQI) eigenvalue solver, and a multigrid in energy preconditioner. The multigroup Krylov solver converges more quickly than Gauss Seidel and enables energy decomposition such that Denovo can scale to hundreds of thousands of cores. The new multigrid in energy preconditioner reduces iteration count for many problem types and takes advantage of the new energy decomposition such that it can scale efficiently. Read More


Topology optimization offers great opportunities to design permanent magnetic systems that have specific external field characteristics. Additive manufacturing of polymer bonded magnets with an end-user 3D printer can be used to manufacture permanent magnets with structures that have been difficult or impossible to manufacture previously. This work combines these two powerful methods to design and manufacture permanent magnetic system with specific properties. Read More


ReaxFF provides a method to model reactive chemical systems in large-scale molecular dynamics simulations. Here, we developed a ReaxFF potential for phosphorus-hydrogen systems. This potential is transferable to a wide range of phosphorus-hydrogen systems, including the P-H molecules, bulk black phosphorus, the atomic-thin black phosphorus layers, i. Read More


Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor $f$ that has typical values of 4-20 for atomic resolution simulations. Read More


We performed highly resolved one-dimensional fully compressible Navier-Stokes simulations of heat-release-induced compression waves in near-critical CO2. The computational setup, inspired by the experimental setup of Miura et al., Phys. Read More


We study the nonequilibrium phase transitions in the one-dimensional duplet creation model using the $n-$site approximation scheme. We find the phase diagram in the space of parameters $(\gamma,D)$, where $\gamma$ is the particle decay probability and $D$ is the diffusion probability. Through data $(1\leq n \leq 18)$ we show that in the limit $n\rightarrow \infty$ the model presents a continuous transition of active state for inactive state (absorbing state) for any value of $0\leq D \leq1$. Read More


A new second-order numerical scheme based on an operator splitting is proposed for the Godunov-Peshkov-Romenski model of continuum mechanics. The homogeneous part of the system is solved with a finite volume method based on a WENO reconstruction, and the temporal ODEs are solved using some analytic results presented here. Whilst it is not possible to attain arbitrary-order accuracy with this scheme (as with ADER-WENO schemes used previously), the attainable order of accuracy is often sufficient, and solutions are computationally cheap when compared with other available schemes. Read More


PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on $A\beta_{25-33}$ fragments and their cross-seeding with $IAPP_{20-29}$ isoforms. Read More


Due to the exponential growth of the state space of coupled quantum systems it is not possible, in general, to numerically store the state of a very large number of quantum systems within a classical computer. We demonstrate a method for modelling the dynamical behaviour of measurable quantities for very large numbers of interacting quantum systems. Our approach makes use of a symbolic non-commutative algebra engine that we have recently developed in conjunction with the well-known Ehrenfest theorem. Read More


Coalescence of liquid droplets on a substrate has been studied extensively, but primarily the interface movement has been in focus. Here we use computer simulations to investigate coalescence of droplets immersed in another liquid, in an inertia-dominated regime. It is found that qualitatively the dynamics is similar to coalescence in air, with similar self-similar growth laws, though quantitative differences appear. Read More


We formulate a Data Driven Computing paradigm, termed max-ent Data Driven Computing, that generalizes distance-minimizing Data Driven Computing and is robust with respect to outliers. Robustness is achieved by means of clustering analysis. Specifically, we assign data points a variable relevance depending on distance to the solution and on maximum-entropy estimation. Read More


Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive molecular dynamics which aims to integrate a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. Read More