Functional holography analysis: Simplifying the complexity of dynamical networks (2008)
Itay Baruchi, Danny Grossman, Vladislav Volman, Vernon L. Towle, Eshel Ben-Jacob
We present a novel functional holography (FH) analysis devised to study the dynamics of task-performing biological and man-made dynamical networks. The latter term refers to networks composed of...
Vladislav Volman, Itay Baruchi, Eshel Ben-jacob
Abstract. We compare the recorded activity of cultured neuronal networks with hybridized model simulations, in which the model neurons are driven by the recorded activity of special neurons. The...
Abstract Functional Holography Analysis: Simplifying the Complexity of Dynamical Networks (2008)
Itay Baruchi, Danny Grossman, Vladislav Volman, John Hunter, Vernon L. Towle, Eshel Ben-jacob
We present a novel functional holography (FH) analysis devised to study the dynamics of taskperforming biological and man-made dynamical networks. The latter term refers to networks composed of...
Coexistence of amplitude and frequency modulations in intracellular calcium dynamics (2008)
De Pitta, Maurizio, Volman, Vladislav, Levine, Herbert, Pioggia, Giovanni, De Rossi, Danilo, Ben-Jacob, Eshel
The complex dynamics of intracellular calcium regulates cellular responses to information encoded in extracellular signals. Here, we study the encoding of these external signals in the context of the...
Collective Plasticity and Individual Stability in Cultured Neuronal Networks (2008)
Nadav Raichman, Vladislav Volman, Eshel Ben-jacob
Temporal fingerprint Cultured neuronal networks generate spontaneous activity in the form of synchronized bursting events (SBEs) – short time events during which most of the recorded neurons fire...
Arnon Arazi, Eshel Ben-jacob, Uri Yechiali
Abstract We consider a Jackson-type network comprised of 2 queues having state-dependent service rates, in which the queue lengths evolve periodically, exhibiting noisy cycles. To reduce this noise a...
A Quantitative Study of the Dynamics of Adaptive Mutation Appearance (2007)
Ido Golding, Barbara Drossel, Yoash Shapira, Eshel Ben-jacob
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Bacterial Cooperative Organization Under Antibiotic Stress (2007)
Physica A, Eshel Ben-jacob, Inon Cohen, Ido Golding, David L. Gutnick, ...
Bacteria have developed sophisticated modes of cooperative behavior to cope with unfavorable environmental conditions. Here we report the e#ect of antibiotic stress on the colonial development of...
Studies of Bacterial Cooperative Organization (2007)
Ido Golding, Inon Cohen, Eshel Ben-jacob
Introduction During the course of evolution, bacteria have developed sophisticated cooperative behavior and intricate communication capabilities [1--3]. Utilizing these capabilities, bacterial...
Correlated Phenotypic Transitions to Competence in Bacterial Colonies (2007)
Hecht, Inbal, Ben-Jacob, Eshel, Levine, Herbert
Genetic competence is a phenotypic state of a bacterial cell in which it is capable of importing DNA, presumably to hasten its exploration of alternate genes in its quest for survival under stress....
Calcium and synaptic dynamics underlying reverberatory activity in neuronal networks (2007)
Volman, Vladislav, Gerkin, Richard, Lau, Pak-Ming, Ben-Jacob, Eshel, Bi, Guo-Qiang
Persistent activity is postulated to drive neural network plasticity and learning. To investigate its underlying cellular mechanisms, we developed a biophysically tractable model that explains the...
Detecting and localizing the foci in human epileptic seizures (2007)
Ben-Jacob, Eshel, Boccaletti, Stefano, Pomyalov, Anna, Procaccia, Itamar, Towle, Vernon L.
We consider the electrical signals recorded from a subdural array of electrodes placed on the pial surface of the brain for chronic evaluation of epileptic patients before surgical resection. A...
Electro-chemical and biological properties of carbon nanotube based multi-electrode arrays (2007)
Gabay, Tamir, Ben-David, Moti, Kalifa, Itshak, Sorkin, Raya, Abrams, Ze’ev R., Ben-Jacob, Eshel, ...
A novel class of micro-electrodes was fabricated by synthesizing high density carbon nanotube islands on lithographically defined, passivated titanium nitride conductors on a silicon dioxide...
The astrocyte as a gatekeeper of synaptic information transfer (2006)
Volman, Vladislav, Ben-Jacob, Eshel, Levine, Herbert
We present a simple biophysical model for the coupling between synaptic transmission and the local calcium concentration on an enveloping astrocytic domain. This interaction enables the astrocyte to...
Novel type of phase transition in a system of self-driven particles (2006)
Vicsek, Tamas, Czirok, Andras, Ben-Jacob, Eshel, Cohen, Inon, Sochet, Ofer
A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model...
Time-invariant person-specific frequency templates in human brain activity (2006)
Doron, Itai, Hulata, Eyal, Baruchi, Itay, Towle, Vernon L., Ben-Jacob, Eshel
The various human brain tasks are performed at different locations and time scales. Yet, we discovered the existence of time-invariant (above an essential time scale) partitioning of the brain...
Self-engineering capabilities of bacteria (2006)
Ben-Jacob, Eshel, Levine, Herbert
Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize)...
Itay Baruchi, Vernon L. Towle, Eshel Ben-Jacob
A functional holography (FH) approach is introduced for analyzing the complex activity of biological networks in the space of functional correlations. Although the activity is often recorded from...
Physical Schemata Underlying Biological Pattern Formation - Examples, Issues and Strategies (2004)
Levine, Herbert, Ben-Jacob, Eshel
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...
Orit Shefi, Sharon Golebowicz, Eshel Ben-jacob, Amir Ayali
ABSTRACT: Neurite outgrowth and branching patterns are instrumental in dictating the wiring diagram of developing neuronal networks. We study the self-organization of single cultured neurons into...
and Shannon’s mutual information (2002)
Eyal Hulata, Ronen Segev, Eshel Ben-jacob
A method for spike sorting and detection based on wavelet packets
Abstract Available online at www.sciencedirect.com (2002)
Physica A, Nadav Raichman, Ronen Segev, Eshel Ben-jacob
www.elsevier.com/locate/physa Evolvable hardware:genetic search in a physical realm
Sub-micromorphology of the epicuticle of hornets: AFM studies (2002)
Ishay, Jacob S., Litinetsky, Luba, Pertsis, Vitaly, Barkay, Zahava, Ben-Jacob, Eshel
The upper part of the hornet cuticle in the abdominal region reveals several structures. First, situated at intervals of 10 µm or more apart, there are depressions housing a peripheral photoreceptor...
The artistry of bacterial colonies and the antibiotic crisis (2001)
Since the beginning of massive usage of antibiotics during World War II we have witnessed a dramatic evolutionary event-- the emergence of multiple drug resistant bacteria. The bacteria are capable...
A Quantitative Study of the Dynamics of Adaptive Mutation Appearance (2001)
Ido Golding, Barbara Drossel, Yoash Shapira, Eshel Ben-jacob
We present two dynamical models for the appearance of adaptive mutations, which permit a quantitative comparison with experimental observations. The models quantify two alternative pictures: The...
Orientation field model for chiral branching growth of bacterial colonies (2000)
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...
Generic Modeling of Chemotactic Based Self-Wiring of Neural Networks (2000)
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...
Conformation changes and folding of proteins mediated by Davidov's soliton (1999)
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...
Entropy Revisited: the Plausible Role of Gravitation (1999)
Ben-Jacob, Eshel, Hermon, Ziv, Shnirman, Alexsander
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...
Modeling branching and chiral colonial patterning of lubricating bacteria (1999)
Ben-Jacob, Eshel, Cohen, Inon, Golding, Ido, Kozlovsky, Yonathan
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:...
Spatio-selection in Expanding Bacterial Colonies (1999)
Ido Golding, Inon Cohen, Eshel Ben-jacob
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...
Lubricating Bacteria Model for Branching growth of Bacterial Colonies (1999)
Yonathan Kozlovsky, Inon Cohen, Ido Golding, Eshel Ben-jacob
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....
Spatio-selection in Expanding Bacterial Colonies (1998)
Golding, Ido, Cohen, Inon, Ben-Jacob, Eshel
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...
Lubricating Bacteria Model for Branching growth of Bacterial Colonies (1998)
Kozlovsky, Yonathan, Cohen, Inon, Golding, Ido, Ben-Jacob, Eshel
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....
Ben-Jacob, Eshel, Hermon, Ziv, Caspi, Shay
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...
Continuous and discrete models of cooperation in complex bacterial colonies (1998)
Cohen, Inon, Golding, Ido, Kozlovsky, Yonathan, Ben-Jacob, Eshel
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...
Golding, Ido, Kozlovsky, Yonathan, Cohen, Inon, Ben-Jacob, Eshel
Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of...
Generic Modeling of Chemotactic Based Self-Wiring of Neural Networks (1998)
Segev, Ronen, Ben-Jacob, Eshel
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...
From Neurons to Brain: Adaptive Self-Wiring of Neurons (1998)
Segev, Ronen, Ben-Jacob, Eshel
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...
From Neurons to Brain: Adaptive Self-Wiring of Neurons (1998)
Segev, Ronen, Ben-Jacob, Eshel
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...
From Neurons to Brain: Adaptive Self-Wiring of Neurons (1998)
Segev, Ronen, Ben-Jacob, Eshel
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...
From Neurons to Brain: Adaptive Self-Wiring of Neurons (1998)
Segev, Ronen, Ben-Jacob, Eshel
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...
PERGAMON Contributed article (1998)
Generic modeling of chemotactic based self-wiring of neural networks
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...
Physica A, Ido Golding, Yonathan Kozlovsky, Inon Cohen, Eshel Ben-jacob
Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns re#ect bacterial cooperative self-organization and cybernetic processes of...
Modeling Branching and Chiral Colonial Patterning of Lubricating Bacteria (1998)
Eshel Ben-jacob, Inon Cohen, Ido Golding, Yonathan Kozlovsky
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:...
Do Topological Charge Solitons Participate in DNA Activity? (1997)
Hermon, Ziv, Caspi, Shay, Ben-Jacob, Eshel
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...
Self-Wiring of Neural Networks (1997)
Segev, Ronen, Ben-Jacob, Eshel
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...
Ben-Jacob, Eshel, Guinea, Francisco, Hermon, Ziv, Shnirman, Alexander
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...
Charge Solitons in 1-D Arrays of Serially Coupled Josephson Junctions (1996)
Hermon, Ziv, Ben-Jacob, Eshel, Schön, Gerd
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...
Aggregation Patterns in Stressed Bacteria (1995)
Tsimring, Lev, Levine, Herbert, Aranson, Igor, Ben-Jacob, Eshel, Cohen, Inon, Shochet, Ofer
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...
Thermoelectric and thermo-Coulomb effects in tunnel junctions (1992)
Amman, M., Ben-Jacob, Eshel, Cohn, J. L.
We present a study of the thermoelectric effects in tunnel junctions. In particular we calculate the thermoelectric power coefficient S and the Peltier coefficient P. For macroscopic junctions we...
Thermo-Coulomb effects in mesoscopic tunnel junctions (1991)
Amman, M., Ben-Jacob, Eshel, Cohn, J. L.
We present a study of the thermoelectric effect in tunnel junctions. In particular we calculate the thermopower coefficient S and the Peltier coefficient π. For macroscopic junctions we demonstrate...
Low-temperature electronic transport and the Coulomb blockade in oxidized films of bismuth (1990)
Cohn, J. L., Ben-Jacob, Eshel, Uher, Ctirad
We present low-temperature (0.2 T e2.
Charge solitons in 1-D array of mesoscopic tunnel junctions (1989)
Amman, M., Ben-Jacob, Eshel, Mullen, Kieran
We study the dynamics of a one-dimensional array of mesoscopic normal tunnel junctions using the semiclassical picture. We show that the charging effect on a single electron tunneling through a...
Ordered shapes in nonequilibrium growth (1989)
Ben-Jacob, Eshel, Garik, Peter
Patterns observed during nonequilibrium growth display complex ordering on many length scales. We focus on ordered patterns which reflect the interplay of microscopic and macroscopic dynamics. The...
Ben-Jacob, Eshel, Mullen, Kieran, Amman, M.
We present an effective circuit model of a chain of mesoscopic tunnel junctions. We show that the system possesses a soliton solution. The propagation of the soliton corresponds to the tunneling of a...
The dynamics of mesoscopic normal tunnel junctions (1988)
Mullen, Kieran, Gefen, Yuval, Ben-Jacob, Eshel
We first review the dynamics of mesoscopic tunnel junctions within the semiclassical approach, outlining the method and its assumptions. We examine the case of a single junction driven by a constant...
Interfacial pattern formation far from equilibrium (1987)
Ben-Jacob, Eshel, Garik, Peter, Grier, D.
Over the past few years diffusion-controlled systems have been shown to share a common set of interfacial morphologies. The singular nature of the microscopic dynamics of surface tension and kinetic...
New quantum oscillations in current driven small junctions (1985)
Ben-Jacob, Eshel, Gefen, Yuval
We propose a framework of a quantum mechanical description of current driven tunnel junctions. Based on this description we predict several new effects. These effects can be observed for kBT ET e2/C,...
Wavelength Selection in Systems Far from Equilibrium (1982)
Kramer, Lorenz, Ben-Jacob, Eshel, Brand, Helmut, Cross, M. C.
It is shown that for systems developing stationary periodic patterns there exists at most one stable wavelength state if a supercritical region is connected to a subcritical one by the imposition of...
Evaluating putative mechanisms of the mitotic spindle checkpoint
Doncic, Andreas, Ben-Jacob, Eshel, Barkai, Naama
The mitotic spindle checkpoint halts the cell cycle until all chromosomes are attached to the mitotic spindles. Evidence suggests that the checkpoint prevents cell-cycle progression by inhibiting the...
Evaluating putative mechanisms of the mitotic spindle checkpoint
Doncic, Andreas, Ben-Jacob, Eshel, Barkai, Naama
The mitotic spindle checkpoint halts the cell cycle until all chromosomes are attached to the mitotic spindles. Evidence suggests that the checkpoint prevents cell-cycle progression by inhibiting the...
Noise resistance in the spindle assembly checkpoint
Doncic, Andreas, Ben-Jacob, Eshel, Barkai, Naama
Genetically identical cells vary in the amount of expressed proteins even when growing under the same conditions. It is not yet clear how cellular information processing copes with such stochastic...
Self-engineering capabilities of bacteria
Ben-Jacob, Eshel, Levine, Herbert
Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize)...
Deadly competition between sibling bacterial colonies
Be'er, Avraham, Zhang, H. P., Payne, Shelley M., Ben-Jacob, Eshel, Swinney, Harry L.
Bacteria can secrete a wide array of antibacterial compounds when competing with other bacteria for the same resources. Some of these compounds, such as bacteriocins, can affect bacteria of similar...
Reverse Engineering of the Spindle Assembly Checkpoint
Doncic, Andreas, Ben-Jacob, Eshel, Einav, Shmuel, Barkai, Naama
The Spindle Assembly Checkpoint (SAC) is an intracellular mechanism that ensures proper chromosome segregation. By inhibiting Cdc20, a co-factor of the Anaphase Promoting Complex (APC), the...