Cooperative Strategies and Genome Cybernetics in Formation of Complex Bacterial Patterns

1994 ◽  
Vol 367 ◽  
Author(s):  
Eshel Ben-Jacob ◽  
Ofer Shochet ◽  
Inon Cohen ◽  
Adam Tenenbaum ◽  
Andras CzirÓk ◽  
...  
Keyword(s):  
Pattern Formation ◽  
Degrees Of Freedom ◽  
Cooperative Behavior ◽  
Building Blocks ◽  
Growth Conditions ◽  
Living Systems ◽  
Cooperative Strategies ◽  
Additional Level ◽  
Bacterial Patterns ◽  
The Individual

AbstractWe present a study of interfacial pattern formation during growth of bacterial colonies. Growth of bacterial colonies bears similarities but presents an inherent additional level of complexity in comparison with non-living systems. In the former case, the building blocks themselves are living systems, each with its own autonomous self-interest and internal degrees of freedom. The bacteria have developed sophisticated communication channels, which they utilize when growth conditions are tough. Here we present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. We demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. This self-organization of the colony, which can be achieved only via cooperative behavior of the bacteria, may be viewed as the outcome of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony). Some qualitative features of the complex morphologies can be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic “feedback”.

COMMUNICATION, REGULATION AND CONTROL DURING COMPLEX PATTERNING OF BACTERIAL COLONIES

Fractals ◽  
1994 ◽  
Vol 02 (01) ◽  
pp. 15-44 ◽  
Author(s):  
ESHEL BEN-JACOB ◽  
OFER SHOCHET ◽  
ADAM TENENBAUM ◽  
INON COHEN ◽  
ANDRAS CZIRÓK ◽  
...  
Keyword(s):  
Pattern Formation ◽  
Degrees Of Freedom ◽  
Cooperative Behavior ◽  
Building Blocks ◽  
Growth Conditions ◽  
Living Systems ◽  
Self Organization ◽  
Bacterial Colony ◽  
Additional Level ◽  
The Individual

We present a study of interfacial pattern formation during growth of bacterial colonies. Growth of bacterial colony bears similarities to but presents an inherent additional level of complexity compared to non-living systems. In the former case, the building blocks themselves are living systems each with its own autonomous self-interest and internal degrees of freedom. At the same time, efficient adaptation of the colony to adverse growth conditions requires self-organization on all levels — which can be achieved only via cooperative behavior of the bacteria. To do so, the bacteria have developed sophisticated communication channels on all levels. Here we present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. We demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. Efficient response of the colony requires self-organization on all levels, which can be achieved only via cooperative behavior of the bacteria. It can be viewed as the action of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony) in the determination of the emerging pattern. Some qualitative features of the complex morphologies can be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic "feedback."

COOPERATIVE STRATEGIES IN FORMATION OF COMPLEX BACTERIAL PATTERNS

Fractals ◽  
1995 ◽  
Vol 03 (04) ◽  
pp. 849-868 ◽  
Author(s):  
ESHEL BEN-JACOB ◽  
OFER SHOCHET ◽  
INON COHEN ◽  
ADAM TENENBAUM ◽  
ANDRAS CZIRÓK ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Cooperative Behavior ◽  
Growth Conditions ◽  
Bacterial Strains ◽  
Cooperative Strategies ◽  
Continuous Approach ◽  
Complex Patterns ◽  
Bacterial Patterns ◽  
The Individual ◽  
Generic Strategies

In nature, bacterial colonies often must cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication channels on all levels. The result is that a profusion of complex patterns are formed during growth of various bacterial strains and for different environmental conditions. Some qualitative features of the complex morphologies may be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic “feedback”. We present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. The model is an hybridization of the continuous approach (to handle chemicals’ diffusion) and the atomistic approach (each “atom” or “walker” represents 104–105 bacteria). Using the model we demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. Efficient response of the colony requires self-organization on all levels, which can be achieved only via cooperative behavior of the bacteria. It can be viewed as the action of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony) in the determination of the emerging pattern. We show that seemingly unrelated patterns can result from the employment of the same generic strategies.

scholarly journals Inverse Kinematics Data Adaptation to Non-Standard Modular Robotic Arm Consisting of Unique Rotational Modules

2021 ◽  
Vol 11 (3) ◽  
pp. 1203
Author(s):  
Štefan Ondočko ◽  
Jozef Svetlík ◽  
Michal Šašala ◽  
Zdenko Bobovský ◽  
Tomáš Stejskal ◽  
...  
Keyword(s):  
Inverse Kinematics ◽  
Degrees Of Freedom ◽  
Structural Changes ◽  
Kinematic Chain ◽  
Building Blocks ◽  
Robotic Arm ◽  
Six Degrees Of Freedom ◽  
Coordinate Vector ◽  
Mathematical Equations ◽  
The Individual

The paper describes the original robotic arm designed by our team kinematic design consisting of universal rotational modules (URM). The philosophy of modularity plays quite an important role when it comes to this mechanism since the individual modules will be the building blocks of the entire robotic arm. This is a serial kinematic chain with six degrees of freedom of unlimited rotation. It was modeled in three different environments to obtain the necessary visualizations, data, measurements, structural changes measurements and structural changes. In the environment of the CoppeliaSim Edu, it was constructed mainly to obtain the joints coordinates matching the description of a certain spatial trajectory with an option to test the software potential in future inverse task calculations. In Matlab, the model was constructed to check the mathematical equations in the area of kinematics, the model’s simulations of movements, and to test the numerical calculations of the inverse kinematics. Since the equipment at hand is subject to constant development, its model can also be found in SolidWorks. Thus, the model’s existence in those three environments has enabled us to compare the data and check the models’ structural designs. In Matlab and SolidWorks, we worked with the data imported on joints coordinates, necessitating overcoming certain problems related to calculations of the inverse kinematics. The objective was to compare the results, especially in terms of the position kinematics in Matlab and SolidWorks, provided the initial joint coordinate vector was the same.

Mechanically-Tunable Quantum Interference in Ferrocene-Based Single-Molecule Junctions

2020 ◽  
Author(s):  
María Camarasa-Gómez ◽  
Daniel Hernangómez-Pérez ◽  
Michael S. Inkpen ◽  
Giacomo Lovat ◽  
E-Dean Fung ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantum Interference ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Ferrocene Derivative ◽  
Single Molecule Junctions ◽  
Molecule Junction ◽  
Single Molecule Junction ◽  
The Impact ◽  
D Orbitals

Ferrocenes are ubiquitous organometallic building blocks that comprise a Fe atom sandwiched between two cyclopentadienyl (Cp) rings that rotate freely at room temperature. Of widespread interest in fundamental studies and real-world applications, they have also attracted<br>some interest as functional elements of molecular-scale devices. Here we investigate the impact of<br>the configurational degrees of freedom of a ferrocene derivative on its single-molecule junction<br>conductance. Measurements indicate that the conductance of the ferrocene derivative, which is<br>suppressed by two orders of magnitude as compared to a fully conjugated analog, can be modulated<br>by altering the junction configuration. Ab initio transport calculations show that the low conductance is a consequence of destructive quantum interference effects that arise from the hybridization of metal-based d-orbitals and the ligand-based π-system. By rotating the Cp rings, the hybridization, and thus the quantum interference, can be mechanically controlled, resulting in a conductance modulation that is seen experimentally.<br>

Capabilities

2018 ◽  
Author(s):  
Paul F. M. J. Verschure
Keyword(s):  
Building Blocks ◽  
Living Systems ◽  
System Level ◽  
Cognitive Architectures ◽  
Multiple Components ◽  
Perception Action

This chapter introduces the “Capabilities” section of the Handbook of Living Machines. Where the previous section considered building blocks, we recognize that components or modules do not automatically make systems. Hence, in the remainder of this handbook, the emphasis is toward the capabilities of living systems and their emulation in artifacts. Capabilities often arise from the integration of multiple components and thus sensitize us to the need to develop a system-level perspective on living machines. Here we summarize and consider the 14 contributions in this section which cover perception, action, cognition, communication, and emotion, and the integration of these through cognitive architectures into systems that can emulate the full gamut of integrated behaviors seen in animals including, potentially, our own capacity for consciousness.

Fully Automated Parallel Oligonucleotide Synthesizer

2001 ◽  
Vol 66 (8) ◽  
pp. 1299-1314 ◽  
Author(s):  
Michal Lebl ◽  
Christine Burger ◽  
Brett Ellman ◽  
David Heiner ◽  
Georges Ibrahim ◽  
...  
Keyword(s):  
Solid Phase ◽  
Building Blocks ◽  
Solid Support ◽  
Continuous Operation ◽  
Gear Pump ◽  
Oligonucleotide Synthesis ◽  
Center Of Rotation ◽  
Microtiter Plates ◽  
The Individual ◽  
Design And Construction

Design and construction of automated synthesizers using the tilted plate centrifugation technology is described. Wash solutions and reagents common to all synthesized species are delivered automatically through a 96-channel distributor connected to a gear pump through two four-port selector valves. Building blocks and other specific reagents are delivered automatically through banks of solenoid valves, positioned over the individual wells of the microtiterplate. These instruments have the following capabilities: Parallel solid-phase oligonucleotide synthesis in the wells of polypropylene microtiter plates, which are slightly tilted down towards the center of rotation, thus generating a pocket in each well, in which the solid support is collected during centrifugation, while the liquid is expelled from the wells. Eight microtiterplates are processed simultaneously, providing thus a synthesizer with a capacity of 768 parallel syntheses. The instruments are capable of unattended continuous operation, providing thus a capacity of over two millions 20-mer oligonucleotides in a year.

scholarly journals Comparison of Quantitative Morphology of Layered and Arbitrary Patterns: Contrary to Visual Perception, Binary Arbitrary Patterns Are Layered from a Structural Point of View

2021 ◽  
Vol 11 (14) ◽  
pp. 6300
Author(s):  
Igor Smolyar ◽  
Daniel Smolyar
Keyword(s):  
Boolean Function ◽  
Layer Structure ◽  
Central Element ◽  
Morphological Characteristics ◽  
Building Blocks ◽  
Point Of View ◽  
Living Systems ◽  
Seismic Profiles ◽  
Contour Maps ◽  
Anisotropic Layers

Patterns found among both living systems, such as fish scales, bones, and tree rings, and non-living systems, such as terrestrial and extraterrestrial dunes, microstructures of alloys, and geological seismic profiles, are comprised of anisotropic layers of different thicknesses and lengths. These layered patterns form a record of internal and external factors that regulate pattern formation in their various systems, making it potentially possible to recognize events in the formation history of these systems. In our previous work, we developed an empirical model (EM) of anisotropic layered patterns using an N-partite graph, denoted as G(N), and a Boolean function to formalize the layer structure. The concept of isotropic and anisotropic layers was presented and described in terms of the G(N) and Boolean function. The central element of the present work is the justification that arbitrary binary patterns are made up of such layers. It has been shown that within the frame of the proposed model, it is the isotropic and anisotropic layers themselves that are the building blocks of binary layered and arbitrary patterns; pixels play no role. This is why the EM can be used to describe the morphological characteristics of such patterns. We present the parameters disorder of layer structure, disorder of layer size, and pattern complexity to describe the degree of deviation of the structure and size of an arbitrary anisotropic pattern being studied from the structure and size of a layered isotropic analog. Experiments with arbitrary patterns, such as regular geometric figures, convex and concave polygons, contour maps, the shape of island coastlines, river meanders, historic texts, and artistic drawings are presented to illustrate the spectrum of problems that it may be possible to solve by applying the EM. The differences and similarities between the proposed and existing morphological characteristics of patterns has been discussed, as well as the pros and cons of the suggested method.

scholarly journals Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ling Xin ◽  
Xiaoyang Duan ◽  
Na Liu
Keyword(s):  
Building Block ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Single Type ◽  
Hierarchical Assembly ◽  
Optical Responses ◽  
Self Association ◽  
Living Organisms ◽  
Order Structures ◽  
Chiral System

AbstractIn living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale.

scholarly journals Cross-Linking Effects Dictate the Preference of Galectins to Bind LacNAc-Decorated HPMA Copolymers

2021 ◽  
Vol 22 (11) ◽  
pp. 6000
Author(s):  
Sara Bertuzzi ◽  
Ana Gimeno ◽  
Ane Martinez-Castillo ◽  
Marta G. Lete ◽  
Sandra Delgado ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Lectin Binding ◽  
Building Blocks ◽  
Cryo Electron Microscopy ◽  
Hpma Copolymers ◽  
Hydroxypropyl Methacrylamide ◽  
Galectin 3 ◽  
Nmr Methods ◽  
The Individual ◽  
Statistical Effects

The interaction of multi-LacNAc (Galβ1-4GlcNAc)-containing N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers with human galectin-1 (Gal-1) and the carbohydrate recognition domain (CRD) of human galectin-3 (Gal-3) was analyzed using NMR methods in addition to cryo-electron-microscopy and dynamic light scattering (DLS) experiments. The interaction with individual LacNAc-containing components of the polymer was studied for comparison purposes. For Gal-3 CRD, the NMR data suggest a canonical interaction of the individual small-molecule bi- and trivalent ligands with the lectin binding site and better affinity for the trivalent arrangement due to statistical effects. For the glycopolymers, the interaction was stronger, although no evidence for forming a large supramolecule was obtained. In contrast, for Gal-1, the results indicate the formation of large cross-linked supramolecules in the presence of multivalent LacNAc entities for both the individual building blocks and the polymers. Interestingly, the bivalent and trivalent presentation of LacNAc in the polymer did not produce such an increase, indicating that the multivalency provided by the polymer is sufficient for triggering an efficient binding between the glycopolymer and Gal-1. This hypothesis was further demonstrated by electron microscopy and DLS methods.

Systematic Synthesis and Applications of Novel Multi-Degree-of-Freedom Differential Systems

1992 ◽  
Author(s):  
Sridhar Kota ◽  
Srinivas Bidare
Keyword(s):  
Degrees Of Freedom ◽  
Building Blocks ◽  
Degree Of Freedom ◽  
Differential Systems ◽  
Practical Applications ◽  
Epicyclic Gear ◽  
Differential Mechanism ◽  
Long Time ◽  
Gear Trains ◽  
Drive Systems

Abstract A two-degree-of-freedom differential system has been known for a long time and is widely used in automotive drive systems. Although higher degree-of-freedom differential systems have been developed in the past based on the well-known standard differential, the number of degrees-of-freedom has been severely restricted to 2n. Using a standard differential mechanism and simple epicyclic gear trains as differential building blocks, we have developed novel whiffletree-like differential systems that can provide n-degrees of freedom, where n is any integer greater than two. Symbolic notation for representing these novel differentials is also presented. This paper presents a systematic method of deriving multi-degree-of-freedom differential systems, a three and four output differential systems and some of their practical applications.

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