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The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected…
We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…
Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…
While Bayesian neural networks (BNNs) have drawn increasing attention, their posterior inference remains challenging, due to the high-dimensional and over-parameterized nature. To address this issue, several highly flexible and scalable…
Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…
This work proposes an evolutionary computing-based image segmentation approach for analyzing soundness in Additive Friction Stir Deposition (AFSD) processes. Particle Swarm Optimization (PSO) was employed to determine optimal segmentation…
A profile comparison method with position-specific scoring matrix (PSSM) is one of the most accurate alignment methods. Currently, cosine similarity and correlation coefficient are used as scoring functions of dynamic programming to…
Single Pixel (SP) imaging is now a reality in many applications, e.g., biomedical ultrathin endoscope and fluorescent spectroscopy. In this context, many schemes exist to improve the light throughput of these device, e.g., using structured…
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…
State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted on account of the risk of `variational collapse' down to the…
The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal…
Recently, the joint design of optical systems and downstream algorithms is showing significant potential. However, existing rays-described methods are limited to optimizing geometric degradation, making it difficult to fully represent the…
Coherent diffractive imaging (CDI) is widely used to characterize structured samples from measurements of diffracting intensity patterns. We introduce a numerical framework to quantify the precision that can be achieved when estimating any…
Topology optimization techniques have been applied in integrated optics and nanophotonics for the inverse design of devices with shapes that cannot be conceived by human intuition. At optical frequencies, these techniques have only been…
Fluid-Structure Interaction (FSI) is a crucial problem in ocean engineering. The smoothed particle hydrodynamics (SPH) method has been employed recently for FSI problems in light of its Lagrangian nature and its advantage in handling…
Feature selection is used to eliminate redundant features and keep relevant features, it can enhance machine learning algorithm's performance and accelerate computing speed. In various methods, mutual information has attracted increasingly…
Beam orientation optimization (BOO) is a key component in the process of IMRT treatment planning. It determines to what degree one can achieve a good treatment plan quality in the subsequent plan optimization process. In this paper, we have…
Fiber-integrated micro-optical elements promise a scalable approach to photon collection and beam shaping for quantum information processing. Here, we demonstrate single-step fabrication of micro-spherical, micro-spiral, and micro-axicon…
Rational computer-aided design of multiphase polymer materials is vital for rapid progress in many important applications, such as: diagnostic tests, drug delivery, coatings, additives for constructing materials, cosmetics, etc. Several…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…