Computational high-throughput screening of polymeric photocatalysts: exploring the effect of composition, sequence isomerism and conformational degrees of freedom

Degrees Of Freedom ◽

Chemical Space ◽

Low Cost ◽

Computational Screening ◽

Computational Workflow ◽

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

Computational High-Throughput Screening of Polymeric Photocatalysts: Exploring the Effect of Composition, Sequence Isomerism and Conformational Degrees of Freedom

10.26434/chemrxiv.7314929.v4 ◽

2018 ◽

Author(s):

isabelle Heath-Apostolopoulos ◽

Liam Wilbraham ◽

Martijn Zwijnenburg

Keyword(s):

High Throughput ◽

Degrees Of Freedom ◽

Chemical Space ◽

Low Cost ◽

Computational Screening ◽

Computational Workflow ◽

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

Computational High-Throughput Screening of Polymeric Photocatalysts: Exploring the Effect of Composition, Sequence Isomerism and Conformational Degrees of Freedom

10.26434/chemrxiv.7314929.v1 ◽

2018 ◽

Author(s):

isabelle Heath-Apostolopoulos ◽

Liam Wilbraham ◽

Martijn Zwijnenburg

Keyword(s):

High Throughput ◽

Degrees Of Freedom ◽

Chemical Space ◽

Low Cost ◽

Computational Screening ◽

Computational Workflow ◽

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

Computational High-Throughput Screening of Polymeric Photocatalysts: Exploring the Effect of Composition, Sequence Isomerism and Conformational Degrees of Freedom

10.26434/chemrxiv.7314929 ◽

2018 ◽

Author(s):

isabelle Heath-Apostolopoulos ◽

Liam Wilbraham ◽

Martijn Zwijnenburg

Keyword(s):

High Throughput ◽

Degrees Of Freedom ◽

Chemical Space ◽

Low Cost ◽

Computational Screening ◽

Computational Workflow ◽

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

Computational High-Throughput Screening of Polymeric Photocatalysts: Exploring the Effect of Composition, Sequence Isomerism and Conformational Degrees of Freedom

10.26434/chemrxiv.7314929.v2 ◽

2018 ◽

Author(s):

isabelle Heath-Apostolopoulos ◽

Liam Wilbraham ◽

Martijn Zwijnenburg

Keyword(s):

High Throughput ◽

Degrees Of Freedom ◽

Chemical Space ◽

Low Cost ◽

Computational Screening ◽

Computational Workflow ◽

We discuss a low-cost computational workflow for the high-throughput screening of polymeric photocatalysts and demonstrate its utility by applying it to a number of challenging problems that would be difficult to tackle otherwise. Specifically we show how having access to a low-cost method allows one to screen a vast chemical space, as well as to probe the effects of conformational degrees of freedom and sequence isomerism. Finally, we discuss both the opportunities of computational screening in the search for polymer photocatalysts, as well as the biggest challenges.

MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis

SLAS DISCOVERY Advancing Life Sciences ◽

10.1177/2472555217727517 ◽

2017 ◽

Vol 22 (10) ◽

pp. 1246-1252 ◽

Cited By ~ 1

Author(s):

Kishore Kumar Jagadeesan ◽

Simon Ekström

Keyword(s):

Mass Spectrometry ◽

High Throughput ◽

Web Application ◽

Low Cost ◽

Maldi Ms ◽

Ionization Mass ◽

Label Free ◽

Label Free Detection ◽

R Shiny

Recently, mass spectrometry (MS) has emerged as an important tool for high-throughput screening (HTS) providing a direct and label-free detection method, complementing traditional fluorescent and colorimetric methodologies. Among the various MS techniques used for HTS, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides many of the characteristics required for high-throughput analyses, such as low cost, speed, and automation. However, visualization and analysis of the large datasets generated by HTS MALDI-MS can pose significant challenges, especially for multiparametric experiments. The datasets can be generated fast, and the complexity of the experimental data (e.g., screening many different sorbent phases, the sorbent mass, and the load, wash, and elution conditions) makes manual data analysis difficult. To address these challenges, a comprehensive informatics tool called MALDIViz was developed. This tool is an R-Shiny-based web application, accessible independently of the operating system and without the need to install any program locally. It has been designed to facilitate easy analysis and visualization of MALDI-MS datasets, comparison of multiplex experiments, and export of the analysis results to high-quality images.

Computational Method for Simulating Thermoset Polymer Curing and Prediction of Thermophysical Properties

10.26434/chemrxiv.12453989.v1 ◽

2020 ◽

Author(s):

Jeffrey Sanders ◽

Carla E. Estridge ◽

Matthew B Jackson ◽

Thomas JL Mustard ◽

Samuel J. Tucker ◽

...

Keyword(s):

High Throughput ◽

Thermophysical Properties ◽

Simulation Analysis ◽

Low Cost ◽

Polymer Network ◽

Thermomechanical Properties ◽

Computational Method ◽

Cross Linking ◽

Automated Simulation

Thermoset polymers are an area of intense research due to their low cost, ease of processing, environmental resistance, and unique physical properties. The favorable properties of this class of polymers have many applications in aerospace, automotive, marine, and sports equipment industries. Molecular simulations of thermosets are frequently used to model formation of the polymer network, and to predict the thermomechanical properties. These simulations usually require custom algorithms that are not easily accessible to non-experts and not suited for high throughput screening. To address these issues, we have developed a robust cross-linking algorithm that can incorporate different types of chemistries and leverage GPU-enabled molecular dynamics simulations. Automated simulation analysis tools for cross-linking simulations are also presented. Using four well known epoxy/amine formulations as a foundational case study and benzoxazine as an example of how additional chemistries can be modeled, we demonstrate the power of the algorithm to accurately predict curing and thermophysical properties. These tools are able to streamline the thermoset simulation process, opening up avenues to in-silico high throughput screening for advanced material development.

Genomics and Systems Biology.

Blood ◽

10.1182/blood.v112.11.sci-51.sci-51 ◽

2008 ◽

Vol 112 (11) ◽

pp. sci-51-sci-51

Author(s):

Todd R. Golub

Keyword(s):

Gene Expression ◽

High Throughput ◽

Biological Networks ◽

Expression Profiles ◽

Low Cost ◽

Gene Expression Profiles ◽

Gene Expression Signature ◽

Small Molecule Libraries ◽

Approved Drugs

Genomics holds particular potential for the elucidation of biological networks that underlie disease. For example, gene expression profiles have been used to classify human cancers, and have more recently been used to predict graft rejection following organ transplantation. Such signatures thus hold promise both as diagnostic approaches and as tools with which to dissect biological mechanism. Such systems-based approaches are also beginning to impact the drug discovery process. For example, it is now feasible to measure gene expression signatures at low cost and high throughput, thereby allowing for the screening libraries of small molecule libraries in order to identify compounds capable of perturbing a signature of interest (even if the critical drivers of that signature are not yet known). This approach, known as Gene Expression-Based High Throughput Screening (GE-HTS), has been shown to identify candidate therapeutic approaches in AML, Ewing sarcoma, and neuroblastoma, and has identified tool compounds capable of inhibiting PDGF receptor signaling. A related approach, known as the Connectivity Map (www.broad.mit.edu/cmap) attempts to use gene expression profiles as a universal language with which to connect cellular states, gene product function, and drug action. In this manner, a gene expression signature of interest is used to computationally query a database of gene expression profiles of cells systematically treated with a large number of compounds (e.g., all off-patent FDA-approved drugs), thereby identifying potential new applications for existing drugs. Such systems level approaches thus seek chemical modulators of cellular states, even when the molecular basis of such altered states is unknown.

Parallel Compression Is a Fast Low-Cost Assay for the High-Throughput Screening of Mechanosensory Cytoskeletal Proteins in Cells

ACS Applied Materials & Interfaces ◽

10.1021/acsami.7b04622 ◽

2017 ◽

Vol 9 (34) ◽

pp. 28168-28179 ◽

Cited By ~ 1

Author(s):

Chunguang Miao ◽

Eric S. Schiffhauer ◽

Evelyn I. Okeke ◽

Douglas N. Robinson ◽

Tianzhi Luo

Keyword(s):

High Throughput ◽

Low Cost ◽

Cytoskeletal Proteins ◽

In Cells

Multiphasic construct studied in an ectopic osteochondral defect model

Journal of The Royal Society Interface ◽

10.1098/rsif.2014.0184 ◽

2014 ◽

Vol 11 (95) ◽

pp. 20140184 ◽

Cited By ~ 39

Author(s):

June E. Jeon ◽

Cédryck Vaquette ◽

Christina Theodoropoulos ◽

Travis J. Klein ◽

Dietmar W. Hutmacher

Keyword(s):

High Throughput ◽

Osteochondral Defect ◽

Low Cost ◽

Current Model ◽

Large Animal ◽

Micro Computed Tomography ◽

Defect Model ◽

Osteochondral Repair

In vivo osteochondral defect models predominantly consist of small animals, such as rabbits. Although they have an advantage of low cost and manageability, their joints are smaller and more easily healed compared with larger animals or humans. We hypothesized that osteochondral cores from large animals can be implanted subcutaneously in rats to create an ectopic osteochondral defect model for routine and high-throughput screening of multiphasic scaffold designs and/or tissue-engineered constructs (TECs). Bovine osteochondral plugs with 4 mm diameter osteochondral defect were fitted with novel multiphasic osteochondral grafts composed of chondrocyte-seeded alginate gels and osteoblast-seeded polycaprolactone scaffolds, prior to being implanted in rats subcutaneously with bone morphogenic protein-7. After 12 weeks of in vivo implantation, histological and micro-computed tomography analyses demonstrated that TECs are susceptible to mineralization. Additionally, there was limited bone formation in the scaffold. These results suggest that the current model requires optimization to facilitate robust bone regeneration and vascular infiltration into the defect site. Taken together, this study provides a proof-of-concept for a high-throughput osteochondral defect model. With further optimization, the presented hybrid in vivo model may address the growing need for a cost-effective way to screen osteochondral repair strategies before moving to large animal preclinical trials.