Related papers: Resolution exchange simulation
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Near term quantum computers suffer from the presence of different noise sources. In order to mitigate for this effect and acquire results with significantly better accuracy, there is the urge of designing efficient error correction or error…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
Despite the increasing prevalence of vector observations, computation of optimal experimental design for multi-response models has received limited attention. To address this problem within the framework of approximate designs, we introduce…
Recently Quantum Computation has generated a lot of interest due to the discovery of a quantum algorithm which can factor large numbers in polynomial time. The usefulness of a quantum com puter is limited by the effect of errors. Simulation…
Proposals for near-term experiments in quantum chemistry on quantum computers leverage the ability to target a subset of degrees of freedom containing the essential quantum behavior, sometimes called the active space. This approximation…
Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of…
Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
The use of high-fidelity computational simulations promises to enable high-throughput hypothesis testing and optimisation of cancer therapies. However, increasing realism comes at the cost of increasing computational requirements. This…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Peptide Optimization is a highly complex problem and it takes very long time of computation. This optimization process uses many software applications in a cluster running GNU/Linux Operating System that perform special tasks. The…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
High-fidelity physics simulations are powerful tools in the design and optimization of charged particle accelerators. However, the computational burden of these simulations often limits their use in practice for design optimization and…
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…
RECAST is an analysis reinterpretation framework; since analyses are often sensitive to a range of models, RECAST can be used to constrain the plethora of theoretical models without the significant investment required for a new analysis.…
Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global…