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Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
Adaptive finite elements combined with geometric multigrid solvers are one of the most efficient numerical methods for problems such as the instationary Navier-Stokes equations. Yet despite their efficiency, computations remain expensive…
Particle accelerators are among the largest, most complex devices. To meet the challenges of increasing energy, intensity, accuracy, compactness, complexity and efficiency, increasingly sophisticated computational tools are required for…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
This problem was solved within the framework of the grant project "Solving of problems of cluster analysis with application of parallel algorithms and cloud technologies" in the Institute of Mathematics and Mathematical Modelling in Almaty.…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
Polymer simulation with both accuracy and efficiency is a challenging task. Machine learning (ML) forcefields have been developed to achieve both the accuracy of ab initio methods and the efficiency of empirical force fields. However,…
The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…
Fitting complicated models to large datasets is a bottleneck of many analyses. We present GooFit, a library and tool for constructing arbitrarily-complex probability density functions (PDFs) to be evaluated on nVidia GPUs or on multicore…
A brief review is presented of the scaling of complex fluids, polymers and polyelectrolytes in solution and in confined geometry, in thermodynamical, structural and rheology properties using equilibrium and nonequilibrium dissipative…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
In this research, atomistic molecular dynamics simulations are combined with mesoscopic phase-field computational methods in order to investigate phase-transformation in polycrystalline Aluminum microstructure. In fact, microstructural…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
This paper presents the RBG-Maxwell framework, a relativistic collisional plasma simulator on GPUs. We provide detailed discussions on the fundamental equations, numerical algorithms, implementation specifics, and key testing outcomes. The…
We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large…