On the importance of length scales in determining the physics of biological systems

2014 ◽  
pp. 53-64
Author(s):  
B. Ashok
2014 ◽  
Author(s):  
Allen Y Chen ◽  
Urartu O.S. Seker ◽  
Michelle Y Lu ◽  
Robert J Citorik ◽  
Timothy Lu

A major challenge in materials science is to create self-assembling, functional, and environmentally responsive materials which can be patterned across multiple length scales. Natural biological systems, such as biofilms, shells, and skeletal tissues, implement dynamic regulatory programs to assemble complex multiscale materials comprised of living and non-living components. Such systems can provide inspiration for the design of heterogeneous functional systems which integrate biotic and abiotic materials via hierarchical self-assembly. Here, we present a synthetic-biology platform for synthesizing and patterning self-assembled functional amyloid materials across multiple length scales with bacterial biofilms. We engineered Escherichia coli curli amyloid production under the tight control of synthetic regulatory circuits and interfaced amyloids with inorganic materials to create a biofilm-based electrical switch whose conductance can be selectively toggled by specific environmental signals. Furthermore, we externally tuned synthetic biofilms to build nanoscale amyloid biomaterials with different structure and composition through the controlled expression of their constituent subunits with artificial gene circuits. By using synthetic cell-cell communication, our engineered biofilms can also autonomously manufacture dynamic materials whose structure and composition change with time. In addition, we show that by combining subunit-level protein engineering, controlled genetic expression of self-assembling subunit proteins, and macroscale spatial gradients, synthetic biofilms can pattern protein biomaterials across multiple length scales. This work lays a foundation for synthesizing, patterning, and controlling composite materials with engineered biological systems. We envision that this approach can be expanded to other cellular and biomaterials contexts for the construction of self-organizing, environmentally responsive, and tunable multiscale composite materials with heterogeneous functionalities. Now published as: Nature Materials, doi:10.1038/nmat3912


2020 ◽  
Vol 31 (14) ◽  
pp. 1498-1511 ◽  
Author(s):  
Grace A. McLaughlin ◽  
Erin M. Langdon ◽  
John M. Crutchley ◽  
Liam J. Holt ◽  
M. Gregory Forest ◽  
...  

The structure of the cytosol across different length scales is a debated topic in cell biology. Here we present tools to measure the physical state of the cytosol by analyzing the 3D motion of nanoparticles expressed in cells. We find evidence that the physical structure of the cytosol is a fundamental source of variability in biological systems.


MRS Bulletin ◽  
1999 ◽  
Vol 24 (12) ◽  
pp. 40-47 ◽  
Author(s):  
J. Kent Blasie ◽  
Peter Timmins

The substantial power of both elastic and inelastic neutron-scattering techniques for the investigation of the structure and dynamics of biological systems and related biomolecular-based materials—as with soft matter in the previous article by Lindner and Wignall—arises primarily from the essentially isomorphous nature of the substitution of deuterium for selected hydrogen atoms in these systems, coupled with the exquisite sensitivity of neutron scattering to this isotopic substitution. Since these systems are comprised of large macromolecules and supramolecular assemblies thereof, their essential structures and dynamics extend from the atomic scale up to very large length scales of the Order of 101–104 Å. Hence neutron sources and neutron-scattering spectrometers optimized for longer wavelength (or “cold”) thermal neutrons are necessary in order to most effectively address the structure and dynamics at the longer length scales inherent to these Systems.The large majority of previous neutron-scattering experiments on biological systems have been performed with reactor neutron sources. Some of the more significant of these are briefly summarized in the following sections. They may be categorized in terms of the nature of the intermolecular order, both orientational and positional, within the System of interest and either the elastic neutron-scattering technique employed to investigate their time-averaged structures or the inelastic neutron-scattering technique employed to investigate their dynamics.


2001 ◽  
Author(s):  
Jeremy A. Levitan ◽  
Dan Good ◽  
Michael J. Sinclair ◽  
Joseph M. Jacobson

Abstract Current microfabrication systems can achieve resolutions of approximately 0.1μm. We present physical methods for creating structures with length scales and characteristic dimensions significantly below current fabrication resolutions. These structures, themselves fabricated in conventional, gross-resolution (greater than 2μm) semiconductor facilities, undergo structural change to create features below the lithography limits of the fabrication process. These devices — dog-boned microfabricated polysilicon fuses — are heated just below melting, and a small perturbation current heats a narrow, necked region of the beam, resulting in fusing. Infrastructure has already been constructed to create gross-resolution structures in microfabrication. Novel processes and mechanisms are needed to utilize these resolutions and create structures capable of addressing biological systems, functioning quantum mechanically, use single electrons, or require extreme speeds.


Author(s):  
Henry S. Slayter

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.


Author(s):  
Nicholas J Severs

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.


2019 ◽  
Vol 3 (5) ◽  
pp. 435-443 ◽  
Author(s):  
Addy Pross

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.


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