| 941. |
- Zhdanov, Vladimir, 1952
(författare)
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Diffusion-limited association of nanoparticles in fluid: Beyond the no-slip boundary conditions
- 2022
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Ingår i: Colloids and Interface Science Communications. - : Elsevier BV. - 2215-0382. ; 46
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Tidskriftsartikel (refereegranskat)abstract
- In the treatments of diffusion-limited association of suspended nanoparticles (NPs), their diffusion coefficients are usually considered to be constant or depend on the interparticle distance as determined by fluid dynamics with the no-slip boundary condition. In the latter case, due to the corresponding slowdown of diffusion at short distances, the association rate constant is smaller than that calculated by ignoring this slowdown and using the diffusion coefficients corresponding to single NPs. The no-slip boundary condition can, however, be violated, and now there is evidence that it may happen more often than one could expect. In such situations, the partial-slip boundary condition is more suitable. Employing the latter boundary condition, I derive herein general integral expressions for the rate constant of association of spherically shaped NPs without and with the NP-NP interaction. Simple analytical results have been obtained in various situations.
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| 942. |
- Zhdanov, Vladimir, 1952
(författare)
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How the partial-slip boundary condition can influence the interpretation of the DLS and NTA data
- 2020
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Ingår i: Journal of Biological Physics. - : Springer Science and Business Media LLC. - 0092-0606 .- 1573-0689. ; 46:2, s. 169-176
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) are widely used to determine the size of biological nanoparticles in liquid. In both cases, one first measures the nanoparticle diffusion coefficient and then converts it to the nanoparticle radius via the Stokes-Einstein relation. This relation is based on the no-slip boundary condition. Now, there is evidence that this condition can be violated in biologically relevant cases (e.g., for vesicles) and that in such situations the partial-slip boundary condition is more suitable. I show (i) how the latter condition can be employed in the context of DLS and NTA and (ii) that the use of the former condition may result in underestimation of the nanoparticle radius by about 10 nm compared with the nominal one.
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| 943. |
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| 944. |
- Öktem, Ozan, 1969-, et al.
(författare)
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A component-wise iterated relative entropy regularization method with updated prior and regularization parameter
- 2007
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Ingår i: Inverse Problems. - : Institute of Physics (IOP). - 0266-5611 .- 1361-6420. ; 23:5, s. 2121-2139
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Tidskriftsartikel (refereegranskat)abstract
- We present a componentwise iterated relative entropy regularization method (COMET) where the prior and regularization parameter could be updated in the iterates. Such a reconstruction method could be useful for multicomponent inverse problems, such as the one occurring in electron tomography. The paper also contains a brief introduction to regularization theory with emphasis on variational based regularization methods, and we rigorously prove that the tolerance-based entropy reconstruction method that occurs in the COMET iterates is a regularization method. We conclude by showing examples of COMET applied to electron tomography data.
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| 945. |
- Örnhag, Marcus Valtonen, et al.
(författare)
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A Unified Optimization Framework for Low-Rank Inducing Penalties
- 2020
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Ingår i: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. - 1063-6919. - 9781728171685 ; , s. 8471-8480
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Konferensbidrag (refereegranskat)abstract
- In this paper we study the convex envelopes of a new class of functions. Using this approach, we are able to unify two important classes of regularizers from unbiased nonconvex formulations and weighted nuclear norm penalties. This opens up for possibilities of combining the best of both worlds, and to leverage each method’s contribution to cases where simply enforcing one of the regularizers are insufficient. We show that the proposed regularizers can be incorporated in standard splitting schemes such as Alternating Direction Methods of Multipliers (ADMM), and other subgradient methods. Furthermore, we provide an efficient way of computing the proximal operator. Lastly, we show on real non-rigid structure-from-motion (NRSfM) datasets, the issues that arise from using weighted nuclear norm penalties, and how this can be remedied using our proposed method.
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| 946. |
- Abdallah, Nancy, et al.
(författare)
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Free resolutions and Lefschetz properties of some Artin Gorenstein rings of codimension four
- 2024
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Ingår i: Journal of symbolic computation. - 0747-7171 .- 1095-855X. ; 121, s. 102257-102257
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Tidskriftsartikel (refereegranskat)abstract
- In (Stanley, 1978), Stanley constructs an example of an Artinian Gorenstein (AG) ring A with non-unimodal H-vector (1,13,12,13,1). Migliore-Zanello show in (Migliore and Zanello, 2017) that for regularity r=4, Stanley's example has the smallest possible codimension c for an AG ring with non-unimodal H-vector.The weak Lefschetz property (WLP) has been much studied for AG rings; it is easy to show that an AG ring with non-unimodal H-vector fails to have WLP. In codimension c=3 it is conjectured that all AG rings have WLP. For c=4, Gondim shows in (Gondim, 2017) that WLP always holds for r≤4 and gives a family where WLP fails for any r≥7, building on Ikeda's example (Ikeda, 1996) of failure for r=5. In this note we study the minimal free resolution of A and relation to Lefschetz properties (both weak and strong) and Jordan type for c=4 and r≤6.
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| 947. |
- Abenius, Tobias, 1979
(författare)
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Towards Precision Medicine: Exploiting Genetic Variation in Tumours by Inferring Multitype Gene Regulatory Networks
- 2019
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Precision medicine aims to customize treatment to a patient given measured genetic or other molecular data for diagnostics. In cancer, optimal medical treatment, depends on how far the disease has progressed, type and subtype of cancer and, the individual tumor’s circumstances. Finding large-scale genome-wide models for cancer tumours comes with several challenges including, but not limited to, the relatively small size of the cohort compared to the vast number of genes. In this licentiate thesis, using DNA copy number aberration (CNA), mRNA expression data and survival data, methods were developed to adress some of the issues along the path towards useful large-scale models. In paper I, two related models were suggested that incorporate these data types. To allow large-scale computations a new LASSO solver based on Cyclic Coordinate Descent were coded in C/BLAS for both R and Matlab. A set of validation techniques were used and the solutions to the models could find both previously known genes involved in cancer as well as new candidate targets for intervention, predicting survival length and further elucidated the connectome. One of these candidate targets were verified in vitro. In paper II, the techniques and the software developed in paper I, were further refined in the form of R packages and exposed in a book chapter as a hands on tutorial. In paper III, efforts were made to increase the likelihood of reproducibility and save both human and machine time in calculations and report writing. Having calculations splitted into interdependent blocks and caching computations, results in a dynamic update of reports which change if data or analysis change. This allows for certain in silico issues in the reproducibility process to be mitigated. In paper IV, a model was developed to find similarites and differences between cancer types or subtypes. Potential benefits are to further elucidate the workings of the gene regulatory networks in cancer for multiple cohort clusters at any granularity by exploiting the accumulative statistical strength for coinciding cross-type subnetworks increasing the available sample size while keeping the resolution at a type or sub-type specific level. Known genes relevant to cancer appear in the models and the networks inferred disclose candidate hub genes, connections of interest for candidate sub-hub interventions predictors for survival important for selection of therapy. A generalization to pairwise fused LASSO were used as a model and a solver were implemented using Split Bregman optimization and parallel computations in C/BLAS. I conclude that the tools and models presented may aid in accelerating the system biology loop and provide insights into the biology of cancers, be it type, subtype or as more data come in, even smaller groups.
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| 948. |
- Abola, Benard, et al.
(författare)
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A Variant of Updating Page Rank in Evolving Tree graphs
- 2019
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Ingår i: Proceedings of 18th Applied Stochastic Models and Data Analysis International Conference with the Demographics 2019 Workshop, Florence, Italy: 11-14 June, 2019. - : ISAST: International Society for the Advancement of Science and Technology. - 9786185180331 ; , s. 31-49
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Konferensbidrag (refereegranskat)abstract
- PageRank update refers to the process of computing new PageRank values after change(s) (addition or removal of links/vertices) has occurred in real life networks. The purpose of the updating is to avoid recalculating the values from scratch. To efficiently carry out the update, we consider PageRank as the expected number of visits to target vertex if multiple random walks are performed, starting at each vertex once and weighing each of these walks by a weight value. Hence, it might be looked at as updating non-normalised PageRank. In the proposed approach, a scaled adjacency matrix is sequentially updated after every change and the levels of the vertices being updated as well. This enables sets of internal and sink vertices dependent on their roots or parents, thus vector-vector product can be performed sequentially since there are no infinite steps from one vertex to the other.
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| 949. |
- Abola, Benard, et al.
(författare)
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A Variant of Updating PageRank in Evolving Tree Graphs
- 2021
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Ingår i: Applied Modeling Techniques and Data Analysis 1. - : John Wiley & Sons, Inc. Hoboken, NJ, USA. - 9781786306739 - 9781119821564 ; , s. 3-22
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Bokkapitel (refereegranskat)abstract
- A PageRank update refers to the process of computing new PageRank valuesafter a change(s) (addition or removal of links/vertices) has occurred in real-lifenetworks. The purpose of updating is to avoid re-calculating the values from scratch.To efficiently carry out the update, we consider PageRank to be the expected numberof visits to a target vertex if multiple random walks are performed, starting at eachvertex once and weighing each of these walks by a weight value. Hence, it mightbe looked at as updating a non-normalized PageRank. We focus on networks of treegraphs and propose an approach to sequentially update a scaled adjacency matrix afterevery change, as well as the levels of the vertices. In this way, we can update thePageRank of affected vertices by their corresponding levels.
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| 950. |
- Abola, Benard, 1971-, et al.
(författare)
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PageRank in evolving tree graphs
- 2018
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Ingår i: Stochastic Processes and Applications. - Cham : Springer. - 9783030028244 ; , s. 375-390
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Bokkapitel (refereegranskat)abstract
- In this article, we study how PageRank can be updated in an evolving tree graph. We are interested in finding how ranks of the graph can be updated simultaneously and effectively using previous ranks without resorting to iterative methods such as the Jacobi or Power method. We demonstrate and discuss how PageRank can be updated when a leaf is added to a tree, at least one leaf is added to a vertex with at least one outgoing edge, an edge added to vertices at the same level and forward edge is added in a tree graph. The results of this paper provide new insights and applications of standard partitioning of vertices of the graph into levels using breadth-first search algorithm. Then, one determines PageRanks as the expected numbers of random walk starting from any vertex in the graph. We noted that time complexity of the proposed method is linear, which is quite good. Also, it is important to point out that the types of vertex play essential role in updating of PageRank.
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