scholarly journals Programming Self-Assembled Materials With DNA-Coated Colloids

2021 ◽  
Vol 9 ◽  
Author(s):  
Tianran Zhang ◽  
Dengping Lyu ◽  
Wei Xu ◽  
Yijiang Mu ◽  
Yufeng Wang
Keyword(s):  
Structural Information ◽  
Surface Shape ◽  
Diamond Structure ◽  
Significant Progress ◽  
Key Factors ◽  
Intelligent Materials ◽  
Coated Particles ◽  
Grand Challenges ◽  
Tunable Interactions ◽  
Building Elements

Introducing the concept of programmability paves the way for designing complex and intelligent materials, where the materials’ structural information is pre-encoded in the components that build the system. With highly tunable interactions, DNA-coated particles are promising building elements to program materials at the colloidal scale, but several grand challenges have prevented them from assembling into the desired structures and phases. In recent years, the field has seen significant progress in tackling these challenges, which has led to the realization of numerous colloidal structures and dynamics previously inaccessible, including the desirable colloidal diamond structure, that are useful for photonic and various other applications. We review this exciting progress, focusing in detail on how DNA-coated colloids can be designed to have a sophisticatedly tailored surface, shape, patches, as well as controlled kinetics, which are key factors that allow one to program in principle a limitless number of structures. We also share our view on how the field may be directed in future.

scholarly journals Analysis of several key factors influencing deep learning-based inter-residue contact prediction

2019 ◽  
Author(s):  
Tianqi Wu ◽  
Jie Hou ◽  
Badri Adhikari ◽  
Jianlin Cheng
Keyword(s):  
Deep Learning ◽  
Structural Information ◽  
Protein Structures ◽  
Supplementary Information ◽  
Prediction Methods ◽  
Key Factors ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Contact Prediction ◽  
Ab Initio Approach

Abstract Motivation Deep learning has become the dominant technology for protein contact prediction. However, the factors that affect the performance of deep learning in contact prediction have not been systematically investigated. Results We analyzed the results of our three deep learning-based contact prediction methods (MULTICOM-CLUSTER, MULTICOM-CONSTRUCT and MULTICOM-NOVEL) in the CASP13 experiment and identified several key factors [i.e. deep learning technique, multiple sequence alignment (MSA), distance distribution prediction and domain-based contact integration] that influenced the contact prediction accuracy. We compared our convolutional neural network (CNN)-based contact prediction methods with three coevolution-based methods on 75 CASP13 targets consisting of 108 domains. We demonstrated that the CNN-based multi-distance approach was able to leverage global coevolutionary coupling patterns comprised of multiple correlated contacts for more accurate contact prediction than the local coevolution-based methods, leading to a substantial increase of precision by 19.2 percentage points. We also tested different alignment methods and domain-based contact prediction with the deep learning contact predictors. The comparison of the three methods showed deeper sequence alignments and the integration of domain-based contact prediction with the full-length contact prediction improved the performance of contact prediction. Moreover, we demonstrated that the domain-based contact prediction based on a novel ab initio approach of parsing domains from MSAs alone without using known protein structures was a simple, fast approach to improve contact prediction. Finally, we showed that predicting the distribution of inter-residue distances in multiple distance intervals could capture more structural information and improve binary contact prediction. Availability and implementation https://github.com/multicom-toolbox/DNCON2/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Molecular Packing Interaction in DNA Crystals

Crystals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1093
Author(s):  
Amen Shamim ◽  
Nazia Parveen ◽  
Vinod Kumar Subramani ◽  
Kyeong Kyu Kim
Keyword(s):  
Crystal Packing ◽  
Structural Information ◽  
Key Factors ◽  
Factors Affecting ◽  
Space Groups ◽  
Dna Crystals ◽  
Dna Crystallography ◽  
Packing Interactions ◽  
Packing Interaction

DNA crystallography provides essential structural information to understand the biochemical and biological functions of oligonucleotides. Therefore, it is necessary to understand the factors affecting crystallization of DNA to develop a strategy for production of diffraction-quality DNA crystals. We analyzed key factors affecting intermolecular interactions in 509 DNA crystals from the Nucleic Acid Database and Protein Databank. Packing interactions in DNA crystals were classified into four categories based on the intermolecular hydrogen bonds in base or backbone, and their correlations with other factors were analyzed. From this analysis, we confirmed that hydrogen bonding between terminal end and mid-region is most common in crystal packing and in high-resolution crystal structures. Interestingly, P212121 is highly preferred in DNA crystals in general, but the P61 space group is relatively abundant in A-DNA crystals. Accordingly, P212121 contains more terminal end-mid-region interactions than other space groups, confirming the significance of this interaction. While metals play a role in the production of a good crystal in B-DNA conformation, their effect is not significant in other conformations. From these analyses, we found that packing interaction and other factors have a strong influence on the quality of DNA crystals and provide key information to predict crystal growth of candidate oligonucleotides.

scholarly journals Exploring the Potential of Electroplated Chips towards Biomedical Sensing and Diagnostics

Proceedings ◽  
2018 ◽  
Vol 2 (13) ◽  
pp. 817 ◽  
Author(s):  
Daria Semenova ◽  
Yuliya E. Silina
Keyword(s):  
Clinical Diagnostics ◽  
Cellular Stress Response ◽  
Clinical Samples ◽  
Significant Progress ◽  
Key Factors ◽  
Factors Affecting ◽  
Surface Functionality ◽  
The Past ◽  
Biomedical Sensing ◽  
Analytical Response

In the past decade the significant progress in the cellular stress response was witnessed. Nevertheless, the development of the minimally-invasive and accurate sensing tools for the identification of the increasing number of potentially relevant species in clinical diagnostics, using smaller sample volumes is a major challenge. Herein, the potential of the electroplated nanomaterials towards biomedical sensing and diagnostics is summarized. The key factors affecting the surface functionality, dimensionality, S/N ratio and analytical response of the prepared chips are highlighted. Furthermore, the application of electroplated chips as a fast “read out” platform for profiling of clinical samples was demonstrated.

scholarly journals Determinants of Inter-Regional Financial Inclusion Heterogeneities in the Philippines

2021 ◽  
Vol 9 (2) ◽  
pp. 83-94
Author(s):  
Je-Al Burguillos ◽  
Danny Cassimon
Keyword(s):  
Central Bank ◽  
The Philippines ◽  
Financial Inclusion ◽  
Gdp Per Capita ◽  
Panel Estimation ◽  
Significant Progress ◽  
Key Factors ◽  
Physical Infrastructure ◽  
Vast Literature ◽  
Per Capita

This study tries to contribute to the vast literature on promoting financial inclusion in Asia by exploring the key factors that affect the deepening of financial inclusion across the 17 regions of the Philippines for the period between 2013 and 2017. Using the regional multidimensional financial inclusion index (FII) that is developed by the Philippine central bank, the Bangko Sentral ng Pilipinas (BSP), the study finds out that significant heterogeneities exist among regions, and that they persist over the period analyzed, suggesting most importantly that the least financially inclusive regions do not show rapid significant progress. Moreover, using different panel estimation techniques, we try to determine the possible factors that affect this inter-regional financial inclusion heterogeneities. Overall, we show that regional GDP per capita, population, a proxy for the availability of physical infrastructure, and the degree of mobile penetration are among the robust factors explaining the financial inclusion variations across these regions in the Philippines for the observed period.

Squeaky Wheels and Unequal Policy

2008 ◽  
Vol 41 (7) ◽  
pp. 921-946 ◽  
Author(s):  
Clayton Thyne ◽  
Erika Moreno
Keyword(s):  
World Bank ◽  
Significant Progress ◽  
Key Factors ◽  
Education Systems ◽  
The World Bank ◽  
Recent Scholarship ◽  
American States ◽  
Executive Authority ◽  
The World

The World Bank has been increasingly involved in reforming Latin America's education systems. However, compliance with World Bank directives varies greatly. Recent scholarship has made significant progress in fashioning an explanation for this variation by focusing on the presence of democracy. This article takes the literature a step further by identifying the mechanism by which democracy matters. Specifically, variations in executive authority are key factors in explaining the adoption of controversial World Bank directives. The authors argue that a government's ability to implement World Bank reforms and overcome popular dissent, if present, is a function of executive authority. They examine executive authority using several measures to test their hypotheses on a 20-year panel of 17 American states from 1980 to 2000. Results indicate that newly democratized governments and strong executives are indeed more successful in passing World Bank reforms.

Measurement and Reduction of Radiation Damage in Frozen Hydrated Crystalline Specimens

1978 ◽  
Vol 36 (3) ◽  
pp. 70-77 ◽  
Author(s):  
R.M. Glaeser ◽  
S.B. Hayward
Keyword(s):  
Diffraction Pattern ◽  
Structural Information ◽  
Structural Disorder ◽  
Structural Features ◽  
Biological Macromolecules ◽  
Diffraction Intensity ◽  
Object Structure ◽  
Specimen Material ◽  
Unit Cells ◽  
Identical Unit

Highly ordered or crystalline biological macromolecules become severely damaged and structurally disordered after a brief electron exposure. Evidence that damage and structural disorder are occurring is clearly given by the fading and eventual disappearance of the specimen's electron diffraction pattern. The fading and disappearance of sharp diffraction spots implies a corresponding disappearance of periodic structural features in the specimen. By the same token, there is a oneto- one correspondence between the disappearance of the crystalline diffraction pattern and the disappearance of reproducible structural information that can be observed in the images of identical unit cells of the object structure. The electron exposures that result in a significant decrease in the diffraction intensity will depend somewhat upon the resolution (Bragg spacing) involved, and can vary considerably with the chemical makeup and composition of the specimen material.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

High-Resolution Scanning Electron Microscopy of Biological Specimens

1988 ◽  
Vol 46 ◽  
pp. 186-187
Author(s):  
M. Müller ◽  
R. Hermann
Keyword(s):  
High Resolution ◽  
Freeze Drying ◽  
Room Temperature ◽  
Structural Information ◽  
Freeze Substitution ◽  
Critical Point Drying ◽  
Sem Study ◽  
Major Factors ◽  
Structural Preservation ◽  
Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

Ultimate resolution and information in electron microscopy

1991 ◽  
Vol 49 ◽  
pp. 496-497
Author(s):  
D. Van Dyck
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Transfer Function ◽  
Information Transfer ◽  
Communication Channel ◽  
Structural Information ◽  
Information Rate ◽  
Noise Power ◽  
Signal Power ◽  
Imaging Device

An (electron) microscope can be considered as a communication channel that transfers structural information between an object and an observer. In electron microscopy this information is carried by electrons. According to the theory of Shannon the maximal information rate (or capacity) of a communication channel is given by C = B log2 (1 + S/N) bits/sec., where B is the band width, and S and N the average signal power, respectively noise power at the output. We will now apply to study the information transfer in an electron microscope. For simplicity we will assume the object and the image to be onedimensional (the results can straightforwardly be generalized). An imaging device can be characterized by its transfer function, which describes the magnitude with which a spatial frequency g is transferred through the device, n is the noise. Usually, the resolution of the instrument ᑭ is defined from the cut-off 1/ᑭ beyond which no spadal information is transferred.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

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