arXiv subjects

Eshel Ben-Jacob

Publications and source records attributed to Eshel Ben-Jacob.

35 records · Page 2Linked to original sources

arXiv2004

Physical Schemata Underlying Biological Pattern Formation - Examples, Issues and Strategies

Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the harnessing of pattern-forming processes of non-equilibrium physics and chemistry. For these systems, the study of biological pattern formation starts with placing a biological phenomenon of interest within the context of the proper pattern-formation schema and then focusing on the ways in which control is exerted to adapt the pattern to the needs of the organism. This approach is illustrated by several examples, notably bacterial colonies (diffusive-growth schema) and intracellular calcium waves (excitable-media schema).

q-bio.CB↗

arXiv2000

Orientation field model for chiral branching growth of bacterial colonies

We present a new reaction-diffusion model for chiral branching growth of colonies of the bacteria Paenibacillus dendritiformis. In our model the bacteria are represented by a density field with non-linear diffusion and a complex scalar field which represents bacterial orientation. The orientation field introduces anisotropy into the flux of bacteria, representing self-propulsion along their long axes. The model can also reproduce tip-splitting growth of other strains (shorter bacteria) of the same species. The model can capture changes of small number of bacteria, thus it can be used to study the open question of transitions between tip-splitting and chiral dendritic growth.

cond-mat↗

arXiv1999

Conformation changes and folding of proteins mediated by Davidov's soliton

We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS) field interacts with another field phi, corresponding to the conformation angles of the protein. The interaction provides the conformation field with the energy needed in order to overcome energy barriers for folding, thus avoiding the need for stochastic thermal activation. Such a transition is therefore a deterministic controled process.The soliton is compensated for its energy loss by absorption of the energy gained in the folding process. This scenario does not change significantly even in the presence of imposed disorder, provided that the initial momentum of the soliton is large enough.

cond-mat↗

arXiv1999

Entropy Revisited: the Plausible Role of Gravitation

We first present open questions related to the foundations of thermodynamics and statistical physics. We then argue that in principle one can not have "closed systems", and that a universal background should exist. We propose that the gravitational field plays this role, due to its vanishing energy-momentum tensor. This leads to a new possible picture, in which entropy and irreversibility in macroscopic systems emerge from their coupling to the background gravitational field.

cond-mat↗

arXiv1999

Modeling branching and chiral colonial patterning of lubricating bacteria

In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via extra-membrane polymers, collective production of extracellular "wetting" fluid for movement on hard surfaces, long range chemical signaling such as quorum sensing and chemotactic (bias of movement according to gradient of chemical agent) signaling, collective activation and deactivation of genes and even exchange of genetic material. Utilizing these capabilities, the colonies develop complex spatio-temporal patterns in response to adverse growth conditions. We present a wealth of branching and chiral patterns formed during colonial development of lubricating bacteria (bacteria which produce a wetting layer of fluid for their movement). Invoking ideas from pattern formation in non-living systems and using ``generic'' modeling we are able to reveal novel survival strategies which account for the salient features of the evolved patterns. Using the models, we demonstrate how communication leads to self-organization via cooperative behavior of the cells. In this regard, pattern formation in microorganisms can be viewed as the result of the exchange of information between the micro-level (the individual cells) and the macro-level (the colony). We mainly review known results, but include a new model of chiral growth, which enables us to study the effect of chemotactic signaling on the chiral growth. We also introduce a measure for weak chirality and use this measure to compare the results of model simulations with experimental observations.

cond-mat↗

arXiv1998

Spatio-selection in Expanding Bacterial Colonies

Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial colonies. Such sectors are spatially segregated sub-populations of mutants. The sectors can be seen both in disk-shaped colonies and in branching colonies. We study the sectors using two models we have used in the past to study bacterial colonies -- a continuous reaction-diffusion model with non-linear diffusion and a discrete ``Communicating Walkers'' model. We find that in expanding colonies, and especially in branching colonies, segregation processes are more likely than in a spatially static population. One such process is the establishment of stable sub- population having neutral mutation. Another example is the maintenance of wild-type population along side with sub-population of advantageous mutants. Understanding such processes in bacterial colonies is an important subject by itself, as well as a model system for similar processes in other spreading populations.

cond-mat↗

arXiv1998

Lubricating Bacteria Model for Branching growth of Bacterial Colonies

Various bacterial strains (e.g. strains belonging to the genera Bacillus, Paenibacillus, Serratia and Salmonella) exhibit colonial branching patterns during growth on poor semi-solid substrates. These patterns reflect the bacterial cooperative self-organization. Central part of the cooperation is the collective formation of lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial density and the concentrations of the relevant chemical fields. This idea has been pursued by a number of groups. Here we present an additional model which specifically includes an evolution equation for the lubricant excreted by the bacteria. We show that when the diffusion of the fluid is governed by nonlinear diffusion coefficient branching patterns evolves. We study the effect of the rates of emission and decomposition of the lubricant fluid on the observed patterns. The results are compared with experimental observations. We also include fields of chemotactic agents and food chemotaxis and conclude that these features are needed in order to explain the observations.

cond-mat↗

arXiv1998

DNA - Nanoelectronics: Realization of a Single Electron Tunneling Transistor and a Quantum Bit Element

Based on the understanding that chemical bonds can act as tunnel junctions in the Coulomb blockade regime, and on the technical ability to coat a DNA strand with metal, we suggest that DNA can be used to built logical devices. We discuss two explicit examples: a Single Electron Tunneling Transistor (SET) and a Quantum Bit Element. These devices would be literally in the nano-meter scale and would be able to operate at room temperature. In addition they would be identical to each other, highly stable and would have a self assembly property.

physics.bio-ph↗

arXiv1998

Continuous and discrete models of cooperation in complex bacterial colonies

We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the elements of the macroscopic pattern. We present two types of models. The first is the Communicating Walkers model, a hybrid model composed of both continuous fields and discrete entities - walkers, which are coarse-graining of the bacteria. Models of the second type are systems of reaction diffusion equations, where the branching of the pattern is due to non-constant diffusion coefficient of the bacterial field. The diffusion coefficient represents the effect of self-generated lubrication fluid on the bacterial movement. We implement the discreteness of the biological system by introducing a cutoff in the growth term at low bacterial densities. We demonstrate that the cutoff does not improve the models in any way. Its only effect is to decrease the effective surface tension of the front, making it more sensitive to anisotropy. We compare the models by introducing food chemotaxis and repulsive chemotactic signaling into the models. We find that the growth dynamics of the Communication Walkers model and the growth dynamics of the Non-Linear diffusion model are affected in the same manner. From such similarities and from the insensitivity of the Communication Walkers model to implicit anisotropy we conclude that the increased discreteness, introduced be the coarse-graining of the walkers, is small enough to be neglected.

cond-mat.dis-nn↗

arXiv1998

Generic Modeling of Chemotactic Based Self-Wiring of Neural Networks

The proper functioning of the nervous system depends critically on the intricate network of synaptic connections that are generated during the system development. During the network formation, the growth cones migrate through the embryonic environment to their targets using chemical communication. A major obstacle in the elucidation of fundamental principles underlying this self-wiring is the complexity of the system being analyzed. Hence much effort is devoted to in-vitro experiments of simpler 2D model systems. In these experiments neurons are placed on Poly-L-Lysine (PLL) surfaces so it is easier to monitor their self-wiring. We developed a model to reproduce the salient features of the 2D systems, inspired by the study of bacterial colony's growth and the aggregation of amoebae. We represent the neurons (each composed of cell's soma, neurites and growth cones) by active elements that capture the generic features of the real neurons. The model also incorporates stationary units representing the cells' soma and communicating walkers representing the growth cones. The stationary units send neurites one at a time, and respond to chemical signaling. The walkers migrate in response to chemotaxis substances emitted by the soma and communicate with each other and with the soma by means of chemotactic ``feedback''. The interplay between the chemo-repulsive and chemo-attractive responses is determined by the dynamics of the walker's internal energy which is controlled by the soma. These features enable the neurons to perform the complex task of self-wiring.

cond-mat.dis-nn↗

arXiv1998

Studies of Bacterial Branching Growth using Reaction-Diffusion Models for Colonial Development

Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during colonial development. One method of modeling is the continuous, or coupled reaction-diffusion approach, in which continuous time evolution equations describe the bacterial density and the concentration of the relevant chemical fields. In the context of branching growth, this idea has been pursued by a number of groups. We present an additional model which includes a lubrication fluid excreted by the bacteria. We also add fields of chemotactic agents to the other models. We then present a critique of this whole enterprise with focus on the models' potential for revealing new biological features.

cond-mat↗

arXiv1998

From Neurons to Brain: Adaptive Self-Wiring of Neurons

During embryonic morpho-genesis, a collection of individual neurons turns into a functioning network with unique capabilities. Only recently has this most staggering example of emergent process in the natural world, began to be studied. Here we propose a navigational strategy for neurites growth cones, based on sophisticated chemical signaling. We further propose that the embryonic environment (the neurons and the glia cells) acts as an excitable media in which concentric and spiral chemical waves are formed. Together with the navigation strategy, the chemical waves provide a mechanism for communication, regulation, and control required for the adaptive self-wiring of neurons.

cond-mat↗

arXiv1997

Do Topological Charge Solitons Participate in DNA Activity?

We present a novel electromagnetic model of DNA molecules, in which the P-bonds act as tunnel junctions and the H-bonds as capacitors. Excess charge in the model gives rise to two coupled modified sine-Gordon equations, which admit topological solitonic excitations. We study the dynamics of the solitons, their effect on the DNA transport properties, and comment about their role in the DNA functioning. We propose specific experiments in order to test our predictions.

physics.bio-ph↗

arXiv1997

Self-Wiring of Neural Networks

In order to form the intricate network of synaptic connections in the brain, the growth cones migrate through the embryonic environment to their targets using chemical communication. As a first step to study self-wiring, 2D model systems of neurons have been used. We present a simple model to reproduce the salient features of the 2D systems. The model incorporates random walkers representing the growth cones, which migrate in response to chemotaxis substances extracted by the soma and communicate with each other and with the soma by means of attractive chemotactic "feedback".

cond-mat.dis-nn↗

arXiv1996

Integer and fractional charge solitons in modulated strips in the fractional quantum Hall regime

We propose the existence and study the solitonic excitations in two kinds of samples in the fractional quantum Hall regime. One is a strip modulated by a one-dimensional array of gates. The other is made of two parallel strips coupled by a one-dimensional array of tunnel barriers. We predict the existence of integer charge solitons in the first case, and fractional charge solitons in the second case. We study the two cases both in the dissipative and in the inertial limits.

cond-mat↗

arXiv1996

Charge Solitons in 1-D Arrays of Serially Coupled Josephson Junctions

We study a 1-D array of Josephson coupled superconducting grains with kinetic inductance which dominates over the Josephson inductance. In this limit the dynamics of excess Cooper pairs in the array is described in terms of charge solitons, created by polarization of the grains. We analyze the dynamics of these topological excitations, which are dual to the fluxons in a long Josephson junction, using the continuum sine-Gordon model. We find that their classical relativistic motion leads to saturation branches in the I-V characteristic of the array. We then discuss the semi-classical quantization of the charge soliton, and show that it is consistent with the large kinetic inductance of the array. We study the dynamics of a quantum charge soliton in a ring-shaped array biased by an external flux through its center. If the dephasing length of the quantum charge soliton is larger than the circumference of the array, quantum phenomena like persistent current and coherent current oscillations are expected. As the characteristic width of the charge soliton is of the order of 100 microns, it is a macroscopic quantum object. We discuss the dephasing mechanisms which can suppress the quantum behaviour of the charge soliton.

cond-mat↗

arXiv1995

Aggregation Patterns in Stressed Bacteria

We study the formation of spot patterns seen in a variety of bacterial species when the bacteria are subjected to oxidative stress due to hazardous byproducts of respiration. Our approach consists of coupling the cell density field to a chemoattractant concentration as well as to nutrient and waste fields. The latter serves as a triggering field for emission of chemoattractant. Important elements in the proposed model include the propagation of a front of motile bacteria radially outward form an initial site, a Turing instability of the uniformly dense state and a reduction of motility for cells sufficiently far behind the front. The wide variety of patterns seen in the experiments is explained as being due the variation of the details of the initiation of the chemoattractant emission as well as the transition to a non-motile phase.

patt-sol↗