scholarly journals Defining the Energetic Costs of Cellular Structures

2019 ◽  
Author(s):  
Gita Mahmoudabadi ◽  
Rob Phillips ◽  
Michael Lynch ◽  
Ron Milo
Keyword(s):  
Opportunity Cost ◽  
Building Blocks ◽  
Fitness Cost ◽  
Cellular Structures ◽  
Energetic Cost ◽  
Energetic Costs ◽  
Evolutionary Trajectory ◽  
Essential Step ◽  
Molecular Building Blocks ◽  
Biomass Components

All cellular structures are assembled from molecular building blocks, and molecular building blocks incur energetic costs to the cell. In an energy-limited environment, the energetic cost of a cellular structure imposes a fitness cost and impacts a cell’s evolutionary trajectory. While the importance of energetic considerations was realized for decades, the distinction between direct energetic costs expended by the cell and potential energy that the cell diverts into cellular biomass components, which we define as the opportunity cost, was not explicitly made, leading to large differences in values for energetic costs of molecular building blocks used in the literature. We describe a framework that defines and separates various components relevant for estimating the energetic costs of molecular building blocks and the resulting cellular structures. This distinction among energetic costs is an essential step towards discussing the conversion of an energetic cost to a corresponding fitness cost.

scholarly journals Visualizing and discovering cellular structures with super-resolution microscopy

Science ◽  
2018 ◽  
Vol 361 (6405) ◽  
pp. 880-887 ◽  
Author(s):  
Yaron M. Sigal ◽  
Ruobo Zhou ◽  
Xiaowei Zhuang
Keyword(s):  
State Of The Art ◽  
Super Resolution ◽  
Building Blocks ◽  
Diffraction Limit ◽  
Three Dimensions ◽  
Cellular Structures ◽  
Nanometer Scale ◽  
Molecular Building Blocks ◽  
Resolution Imaging ◽  
Super Resolution Microscopy

Super-resolution microscopy has overcome a long-held resolution barrier—the diffraction limit—in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.

A First Principles Approach for Partitioning Linear Response Properties into Additive and Cooperative Contributions

2018 ◽  
Author(s):  
Daniel Lambrecht ◽  
Eric Berquist
Keyword(s):  
First Principles ◽  
Linear Response ◽  
Building Blocks ◽  
Field Method ◽  
Response Property ◽  
Response Properties ◽  
Consistent Field ◽  
Molecular Building Blocks ◽  
Self Consistent ◽  
Self Consistent Field

We present a first principles approach for decomposing molecular linear response properties into orthogonal (additive) plus non-orthogonal/cooperative contributions. This approach enables one to 1) identify the contributions of molecular building blocks like functional groups or monomer units to a given response property and 2) quantify cooperativity between these contributions. In analogy to the self consistent field method for molecular interactions, SCF(MI), we term our approach LR(MI). The theory, implementation and pilot data are described in detail in the manuscript and supporting information.

A new molecular building blocks: Synthesis, crystal structure, magnetic and spectroscopic properties of Cu(II) and Ni(II) macrocyclic complexes

Polyhedron ◽  
2011 ◽  
Vol 30 (15) ◽  
pp. 2550-2557 ◽  
Author(s):  
Katarzyna Suracka ◽  
Alina Bieńko ◽  
Jerzy Mroziński ◽  
Rafał Kruszyński ◽  
Dariusz Bieńko ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Building Blocks ◽  
Spectroscopic Properties ◽  
Macrocyclic Complexes ◽  
Molecular Building Blocks

scholarly journals Acid-Catalysed Liquid-to-Solid Transitioning of Arylazoisoxazole Photoswitches

2021 ◽  
Author(s):  
Luuk Kortekaas ◽  
Julian Simke ◽  
Niklas Arndt ◽  
Marcus Böckmann ◽  
Nikos Doltsinis ◽  
...  
Keyword(s):  
Building Blocks ◽  
Vital Role ◽  
Responsive Materials ◽  
Molecular Building Blocks ◽  
Physical Changes

Molecular photoswitches play a vital role in the development of responsive materials. These molecular building blocks are particularly attractive when multiple stimuli can be combined to bring about physical changes,...

A Molecular Artisans Guide to Supramolecular Coordination Complexes and Metal Organic Frameworks

2015 ◽  
Vol 03 (01n02) ◽  
pp. 1540004 ◽  
Author(s):  
Xialu Wu ◽  
David J. Young ◽  
T. S. Andy Hor
Keyword(s):  
Chemical Reactivity ◽  
Metal Organic Frameworks ◽  
Building Blocks ◽  
Coordination Complexes ◽  
Large Molecules ◽  
Molecular Building Blocks ◽  
Supramolecular Coordination ◽  
Metal Organic ◽  
Molecular Synthesis ◽  
And Function

As molecular synthesis advances, we are beginning to learn control of not only the chemical reactivity (and function) of molecules, but also of their interactions with other molecules. It is this basic idea that has led to the current explosion of supramolecular science and engineering. Parallel to this development, chemists have been actively pursuing the design of very large molecules using basic molecular building blocks. Herein, we review the general development of supramolecular chemistry and particularly of two new branches: supramolecular coordination complexes (SCCs) and metal organic frameworks (MOFs). These two fields are discussed in detail with typical examples to illustrate what is now possible and what challenges lie ahead for tomorrow's molecular artisans.

scholarly journals Synthetic protocell biology: from reproduction to computation

2007 ◽  
Vol 362 (1486) ◽  
pp. 1727-1739 ◽  
Author(s):  
Ricard V Solé ◽  
Andreea Munteanu ◽  
Carlos Rodriguez-Caso ◽  
Javier Macía
Keyword(s):  
Current Knowledge ◽  
Building Blocks ◽  
Biochemical Networks ◽  
Cellular Structures ◽  
Biological Complexity ◽  
Artificial Cell ◽  
Future Challenges ◽  
Cooperative Dynamics ◽  
The Origin Of Life ◽  
Review Current

Cells are the building blocks of biological complexity. They are complex systems sustained by the coordinated cooperative dynamics of several biochemical networks. Their replication, adaptation and computational features emerge as a consequence of appropriate molecular feedbacks that somehow define what life is. As the last decades have brought the transition from the description-driven biology to the synthesis-driven biology, one great challenge shared by both the fields of bioengineering and the origin of life is to find the appropriate conditions under which living cellular structures can effectively emerge and persist. Here, we review current knowledge (both theoretical and experimental) on possible scenarios of artificial cell design and their future challenges.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

scholarly journals Rearrangement of spiroderivatives of 1,3-benzo(naphtho)dioxin-4(1)-ones as a new method of synthesis of xanthene bromo derivatives

2021 ◽  
pp. 73-77
Author(s):  
A.V. Kovtun ◽  
◽  
S.A. Varenichenko ◽  
E.V. Zaliznaya ◽  
A.V. Mazepa ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
13C Nmr ◽  
Bromine Atom ◽  
Sodium Perchlorate ◽  
Building Blocks ◽  
Dimethylamino Group ◽  
1H And 13C Nmr ◽  
Molecular Building Blocks ◽  
Derivatives Of ◽  
Fold Excess

We have proposed a method for the synthesis of previously unknown bromo xanthenes using the reagent PBr3/DMF as a rearrangement initiator. Bromo derivatives of xanthenes in the form of organic perchlorates were prepared by reacting the corresponding benzo(naphtho)dioxin-4(1)-ones with a three-fold excess of Vilsmeier-Haack PBr3/DMF reagent at 1100C for 2 hours, followed by the addition of sodium perchlorate. The conditions for the synthesis of formyl derivatives of xanthenes under conditions of acid hydrolysis were selected. The structure of the compounds was confirmed by 1H and 13C NMR spectral data and mass spectrometry. Preliminary studies showed that it is possible to selectively replace the dimethylamino group and the bromine atom with various nucleophiles in bromo derivatives of xanthenes, which opens up wide possibilities for the synthesis of low-molecular building blocks and dyes.

scholarly journals Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication

2021 ◽  
Author(s):  
Paweena Chaoprasid ◽  
Peer Lukat ◽  
Sabrina Mühlen ◽  
Thomas Heidler ◽  
Emerich‐Mihai Gazdag ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Building Blocks ◽  
Cytotoxic Necrotizing Factor ◽  
Molecular Building Blocks
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