Related papers: OptiMic: A tool to generate optimized polycrystall…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
We present the first general purpose framework for marginal maximum a posteriori estimation of probabilistic program variables. By using a series of code transformations, the evidence of any probabilistic program, and therefore of any…
Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modelling. Microtubule and actin filaments are well characterized, and the associated proteins are often known, as well as their abundance and…
The purpose of this note is to clarify the effect of the finite size of spherical particles upon the characteristics of their spatial distribution through a random Poisson process (RPP). This information is of special interest when using…
In unresolved flow CFD-DEM simulations, the porosity values for each CFD cell are determined using a coarse-graining algorithm. While this approach enables coupled simulations of representative numbers of particles, the influence of the…
Freestanding photonic crystals can be used to trap both light and mechanical vibrations. These "optomechanical crystal" structures have already been experimentally demonstrated to yield strong coupling between a photon mode and a phonon…
Calculations of elastic and mechanical characteristics of non-crystalline solids are challenging due to high computation cost of $ab$ $initio$ methods and low accuracy of empirical potentials. We propose a computational technique towards…
With our previous study, the Super-k algorithm, we have introduced a novel way of piecewise-linear classification. While working on the Super-k algorithm, we have found that there is a similar, and simpler way to explain for obtaining a…
The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated…
Constraint-based optimization of microbial strains and model-based bioprocess design have been used extensively to enhance yields in biotechnological processes. However, strain and process optimization are usually carried out in sequential…
A method based on optical interferences for measuring optical nonlinearities is presented. In a proof-of-principle experiment, the technique is applied to the experimental determination of the intensity dependence of the photoionization…
Opals are naturally occurring photonic crystals which can be formed easily using low-cost self-assembly methods. While the optical behaviour of opals has received significant attention over the last number of decades, there is limited…
Crystal structure predictions based on the combination of first-principles calculations and machine learning have achieved significant success in materials science. However, most of these approaches are limited to predicting specific…
In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite…
The rational design of photonic nanostructures consists in anticipating their optical response from simple models or as variations of reference systems. This strategy is limited when different objectives are simultaneously targeted.…
The spatial cosmic matter distribution on scales of a few up to more than a hundred Megaparsec displays a salient and pervasive foamlike pattern. Voronoi tessellations are a versatile and flexible mathematical model for such weblike spatial…
Over the last two decades, scanning tunnelling microscopy (STM) has become one of the most important ways to investigate the structure of crystal surfaces. STM has helped achieve remarkable successes in surface science such as finding the…
Effective transport properties of heterogeneous structures are predicted by geometric microstructural parameters, but these can be difficult to calculate. Here, a boundary element code with a recurrent series method accurately and…
Studying the rapid variability of many astronomical objects is key to understanding the underlying processes at play. However, a combination of limited telescope availability, viewing constraints, and the unpredictable nature of many…
Characterizing the spacing of primary dendrite arms in directionally-solidified microstructures is an important step for developing process-structure-property relationships by enabling the quantification of (i) the influence of processing…