Fast Algorithms for Brownian Dynamics with Hydrodynamic Interactions

In this dissertation, we contributed on three fundamental parts of Brownian dynamics simulations with hydrodynamic interactions. The first part of the dissertation is to derive the formulas for computing the electric field gradients by the new version of fast multipole method(FMM) and to implement them as new functions for existing FMM solvers. In the second part of the dissertation, we discuss how to decompose the far-field Rotne-Prager-Yamakawa potential into four far-field Laplace FMM calls including electrostatic potential, electric field and field gradient terms. A parallelized Rotne-Prager-Yamakawa solver based on the new version of fast multipole method has been developed with tunable accuracy. The solver makes it computationally viable for large-scale, long-time Brownian dynamic simulations with hydrodynamic interactions. In the third part, a model is built toward an accurate description of hydrodynamic effects on the translational and rotational dynamics of complex, rigid macromolecules with arbitrary shape in suspension. The grand diffusion matrix is calculated by employing the bead-shell model for describing the shape and structure of macromolecules in the many-body system. Two fast algorithms based on block conjugate gradient method and the Schur complement method are developed for computing the translational and angular velocities, as well as the displacements and orientations in order to track the trajectories of the macromolecules in the complex structured biological system.Doctor of Philosoph

Image abstraction painting of flow-like stylization

U radu se predstavlja tehnika ne-fotorealističkog prikaza u kojoj se iz fotografije dobiva stilizirana apstraktna slika s tonovima koji se prelijevaju. Zasnovana na Kuwahara filtrima i integralnim spiralnim linijama, naša metoda simultano apstrahira oblike i boje, zadržavajući u isto vrijeme osnovna obilježja slika. Posebno razvijamo metodu proširenja i detekcije ruba i usmjeravamo pažnju na specifična obilježja i rubne dijelove slike. Predloženi je algoritam promjenljiv i iterativan te se stupanj prelijevanja tonova i apstrakcije može regulirati. Eksperimentalni rezultati pokazuju da je učinkovitost naše metode u postizanju koherentne i stilizirane apstrakcije zadovoljavajuća, uz zadržavanje osnovnih obilježja iz zadanih fotografija.This paper presents a non-photorealistic rendering technique for producing flow-like abstraction stylization from a photograph. Based on anisotropic Kuwahara filtering in conjunction with line integral convolution, our method abstracts shapes and colors simultaneously while preserving features of images. In particular, we develop an edge detection and dilation method, to draw attention to salient features and image boundaries. This proposed algorithm is incremental and iterative, and therefore the degree of flow and abstraction can be controlled. Experimental results demonstrate that the effectiveness of our method in producing a coherent and flow-like abstraction stylization is satisfactory yet preserving features and directions from photographs

On Two-Level State-Dependent Routing Polling Systems with Mixed Service

Based on priority differentiation and efficiency of the system, we consider an N+1 queues’ single-server two-level polling system which consists of one key queue and N normal queues. The novel contribution of the present paper is that we consider that the server just polls active queues with customers waiting in the queue. Furthermore, key queue is served with exhaustive service and normal queues are served with 1-limited service in a parallel scheduling. For this model, we derive an expression for the probability generating function of the joint queue length distribution at polling epochs. Based on these results, we derive the explicit closed-form expressions for the mean waiting time. Numerical examples demonstrate that theoretical and simulation results are identical and the new system is efficient both at key queue and normal queues

Repositioning of the global epicentre of non-optimal cholesterol

High blood cholesterol is typically considered a feature of wealthy western countries(1,2). However, dietary and behavioural determinants of blood cholesterol are changing rapidly throughout the world(3) and countries are using lipid-lowering medications at varying rates. These changes can have distinct effects on the levels of high-density lipoprotein (HDL) cholesterol and non-HDL cholesterol, which have different effects on human health(4,5). However, the trends of HDL and non-HDL cholesterol levels over time have not been previously reported in a global analysis. Here we pooled 1,127 population-based studies that measured blood lipids in 102.6 million individuals aged 18 years and older to estimate trends from 1980 to 2018 in mean total, non-HDL and HDL cholesterol levels for 200 countries. Globally, there was little change in total or non-HDL cholesterol from 1980 to 2018. This was a net effect of increases in low- and middle-income countries, especially in east and southeast Asia, and decreases in high-income western countries, especially those in northwestern Europe, and in central and eastern Europe. As a result, countries with the highest level of non-HDL cholesterol-which is a marker of cardiovascular riskchanged from those in western Europe such as Belgium, Finland, Greenland, Iceland, Norway, Sweden, Switzerland and Malta in 1980 to those in Asia and the Pacific, such as Tokelau, Malaysia, The Philippines and Thailand. In 2017, high non-HDL cholesterol was responsible for an estimated 3.9 million (95% credible interval 3.7 million-4.2 million) worldwide deaths, half of which occurred in east, southeast and south Asia. The global repositioning of lipid-related risk, with non-optimal cholesterol shifting from a distinct feature of high-income countries in northwestern Europe, north America and Australasia to one that affects countries in east and southeast Asia and Oceania should motivate the use of population-based policies and personal interventions to improve nutrition and enhance access to treatment throughout the world.Peer reviewe

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Video Texture Synthesis Based on Flow-Like Stylization Painting

The paper presents an NP-video rendering system based on natural phenomena. It provides a simple nonphotorealistic video synthesis system in which user can obtain a flow-like stylization painting and infinite video scene. Firstly, based on anisotropic Kuwahara filtering in conjunction with line integral convolution, the phenomena video scene can be rendered to flow-like stylization painting. Secondly, the methods of frame division, patches synthesis, will be used to synthesize infinite playing video. According to selection examples from different natural video texture, our system can generate stylized of flow-like and infinite video scenes. The visual discontinuities between neighbor frames are decreased, and we also preserve feature and details of frames. This rendering system is easy and simple to implement

Forest Fire Detection via Feature Entropy Guided Neural Network

Forest fire detection from videos or images is vital to forest firefighting. Most deep learning based approaches rely on converging image loss, which ignores the content from different fire scenes. In fact, complex content of images always has higher entropy. From this perspective, we propose a novel feature entropy guided neural network for forest fire detection, which is used to balance the content complexity of different training samples. Specifically, a larger weight is given to the feature of the sample with a high entropy source when calculating the classification loss. In addition, we also propose a color attention neural network, which mainly consists of several repeated multiple-blocks of color-attention modules (MCM). Each MCM module can extract the color feature information of fire adequately. The experimental results show that the performance of our proposed method outperforms the state-of-the-art methods