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Taloni A.,University of Milan | Taloni A.,CNR Institute for Complex Systems | Flomenbom O.,Flomenbom BPS Ltd | Castaneda-Priego R.,University of Guanajuato | Marchesoni F.,University of Camerino
Soft Matter | Year: 2017

The term single file (SF) dynamics refers to the motion of an assembly of particles through a channel with cross-sections comparable to the particles' diameter. Single file diffusion (SFD) is then the diffusion of a tagged particle in a single file, i.e., under the condition that particle passing is not allowed. SFD accounts for a large variety of processes in nature, including diffusion of colloids in synthetic and natural channels, biological motors along molecular chains, electrons in proteins and liquid helium, ions through membranes, just to mention a few examples. Albeit introduced in 1965s, over the last decade the classical notion of SF dynamics has been generalised to account for a more realistic modelling of the particle properties, file geometry, particle-particle and channel-particle interactions, which paves the way to remarkable applications of the SF model, for instance, in the technology of bio-integrated nanodevices. We provide here a comprehensive review of the recent advances in the theory of SF dynamics with the purpose of spurring further experimental work. © The Royal Society of Chemistry.


Flomenbom O.,Flomenbom BPS Ltd | Velonia K.,University of Crete | Cotlet M.,Brookhaven National Laboratory
Biophysical Reviews and Letters | Year: 2013

In this document, we present the articles of the Special Issue on measuring & solving single molecules. These include reviews and articles about the state-of-the-art experimental and mathematical methods and applications in life sciences, biophysics and materials science. Ways of solving pitfalls in this field are presented in various articles. This Special Issue can intrigue, inspire and help scientifically both young and established scientists working in this field. © 2013 World Scientific Publishing Company.


PubMed | CNR Institute for Complex Systems, University of Guanajuato, University of Camerino and Flomenbom BPS Ltd
Type: | Journal: Soft matter | Year: 2017

The term single file (SF) dynamics refers to the motion of an assembly of particles through a channel with cross-sections comparable to the particles diameter. Single file diffusion (SFD) is then the diffusion of a tagged particle in a single file, i.e., under the condition that particle passing is not allowed. SFD accounts for a large variety of processes in nature, including diffusion of colloids in synthetic and natural channels, biological motors along molecular chains, electrons in proteins and liquid helium, ions through membranes, just to mention a few examples. Albeit introduced in 1965s, over the last decade the classical notion of SF dynamics has been generalised to account for a more realistic modelling of the particle properties, file geometry, particle-particle and channel-particle interactions, which paves the way to remarkable applications of the SF model, for instance, in the technology of bio-integrated nanodevices. We provide here a comprehensive review of the recent advances in the theory of SF dynamics with the purpose of spurring further experimental work.


Flomenbom O.,Flomenbom BPS Ltd | Coban G.U.,Dokuz Eylül University | Adiguzel Y.,Istanbul Kemerburgaz University
Biophysical Reviews and Letters | Year: 2016

In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area. © 2016 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd. | Baraban L.,TU Dresden | Baraban L.,Leibniz Institute of Polymer Research | Misko V.,University of Antwerp
Biophysical Reviews and Letters | Year: 2016

This is a commentary on the Special Issue continuation involving "Single File Dynamics and Generalizations in Interdisciplinary Sciences". © 2016 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd | Castaneda-Priego R.,University of Guanajuato | Peeters F.,University of Antwerp
Biophysical Reviews and Letters | Year: 2014

In this document, we present the Special Issue's projects; these include reviews and articles about mathematical solutions and formulations of single-file dynamics (SFD), yet also its computational modeling, experimental evidence, and value in explaining real life occurrences. In particular, we introduce projects focusing on electron dynamics on liquid helium in channels with changing width, on the zig-zag configuration in files with longitudinal movement, on expanding files, on both heterogeneous and slow files, on files with external forces, and on the importance of the interaction potential shape on the particle dynamics along the file. Applications of SFD are of intrinsic value in life sciences, biophysics, physics, and materials science, since they can explain a large diversity of many-body systems, e.g., biological channels, biological motors, membranes, crowding, electron motion in proteins, etc. These systems are explained in all the projects that participate in this topical issue. This Special Issue can therefore intrigue, inspire and advance scientifically young people, yet also those scientists that actively work in this field. © 2014 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd
Biophysical Reviews and Letters | Year: 2014

In this review (appearing in the Special Issue on single file dynamics in biophysics and related extensions), three recently treated variants in file dynamics are presented: files with density that is not fixed, files with heterogeneous particles, and files with slow particles. The results in these files include:• In files with a density law that is not fixed, but decays as a power law with an exponent a the distance from the origin, the particle in the origin mean square displacement (MSD) scales like MSD ~ t[1+a]/2, with a Gaussian probability density function (PDF). This extends the scaling, MSD ~ t1/2, seen in a constant density file.• When, in addition, the particles' diffusion coefficients are distributed like a power law with an exponent γ (around the origin), the MSD follows MSD ~ t[1-γ]/[2/(1+a)-γ], with a Gaussian PDF.• In anomalous files that are renewal, namely, when all particles attempt a jump together, yet, with jump times taken from a PDF that decays as a power law with an exponent -1 -ε, ψ(t) ~ t-1-ε, the MSD scales like the MSD of the corresponding normal file, in the power ε.• In anomalous files of independent particles, the MSD is very slow and scales like MSD ~ log2(t). Even more exciting, the particles form clusters, defining a dynamical phase transition: depending on the anomaly power ε, the percentage of particles in clusters ξ follows (Formula presented.), yet when ε > 1, fluidity rather than clusters is seen.We talk about utilizing these results while focusing on biophysical processes and applications: dynamics in channels, membranes, biosensors, etc. Special Issue Comments: In this article, results about recently suggested variants in single file dynamics appear: heterogeneous files and slow files, yet also, the relevance with biophysical processes. It is related to the Special Issue articles about expansions in files,61 files with force,62 and the zig zag occurrences in files.63 © 2014 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd
Biophysical Reviews and Letters | Year: 2013

In this article, we talk about the ways that scientists can solve single molecule trajectories. Solving single molecules, that is, finding the model from the data, is complicated at least as much as measuring single molecules. We must filter the noise and take care of every step in the analysis when constructing the most accurate model from the data. Here, we present valuable solutions. Ways that solve clean discrete data are first presented. We review here our reduced dimensions forms (RDFs): unique models that are canonical forms of discrete data, and the statistical and numerical toolbox that builds a RDF from finite, clean, two-state data. We then review our most recent filter that "tackles" the noise when measuring two state noisy photon trajectories. The filter is a numerical algorithm with various special statistical treatments that is based on a general likelihood function that we have developed recently. We show the strengths of the filter (also over other approaches) and talk about its various new variants. This filter (with minor adjustments) can solve the noise in any discrete state trajectories, yet, extensions are needed in "tackling" the noise from other data, e.g. continuous data. Only the combined procedures enable creating the most accurate model from noisy discrete trajectories from single molecules. These concepts and methods (with adjustments) are valuable also when solving continuous trajectories and fluorescence resonance energy transfer trajectories. We also present a set of simple methods that can help any scientist with treating the trajectory perhaps encouraging applying the involved methods. The involved methods will appear in software that we are developing now, helping therefore the experimentalists utilizing these methods on real data. Comparisons with other known methods in this field are made. Special Issue Comment: This article about mathematical treatments when solving single molecules is related to the reviews in this Special Issue about measuring enzymes67 and about FRET experiments2 and about the software QUB.6 © 2013 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd
Biophysical Reviews and Letters | Year: 2015

Modeling the dynamics in nations from economical and sociological perspectives is a central theme in economics and sociology. Accurate models can predict and therefore help all the world's citizens. Yet, recent years have show that the current models are missing. Here, we develop a dynamical society-deciders model that can explain the stability in a nation, based on concepts from dynamics, ecology and socio-econo-physics; a nation has two groups that interconnect, the deciders and the society. We show that a nation is either stable or it collapses. This depends on just two coefficients that we relate with sociological and economical indicators. We define a new socio-economic indicator, fairness. Fairness can measure the stability in a nation and how probable a change favoring the society is. We compute fairness among all the world's nations. Interestingly, in comparison with other indicators, fairness shows that the USA loses its rank among Western democracies, India is the best among the 15 most populated nations, and Egypt, Libya and Tunisia have significantly improved their rankings as a result of recent revolutions, further increasing the probability of additional positive changes. Within the model, long lasting crises are solved rather than with increasing governmental spending or cuts with regulations that reduce the stability of the deciders, namely, increasing fairness, while, for example, shifting wealth in the direction of the people, and therefore increasing further opportunities. © 2015 World Scientific Publishing Company.


Flomenbom O.,Flomenbom BPS Ltd.
Biophysical Reviews and Letters | Year: 2016

We derive the general scaling law of the mean first passage time (MFPT) in single file dynamics; the process where many real particles move in a channel of length L with absorbing boundaries, where the particles and the channel have about the same cross section. We derive the relation MFPT f(n)MFPTfree, here we compute the MFPT when the channel is free (all particles are absorbed, where the average is over many trajectories), n is the number of particles in the channel at initiation, f(n) is the many-particle effect and the quantity MFPTfree is the MFPT of the free particle. When at initiation the density is fixed in basic files f(n) n and therefore e.g. MFPT L2.5 (basic stochastic dynamics). We also compute the MFPT in diverse files; for example, in a file with heterogeneous particles, in deterministic files, in slow files and in files with long-range interactions. When the particle density is not fixed yet scales with 1/length from the origin, f(n) < n; yet, interactions might increase (attractive) or decrease (repulsive) the many-particle effect relative to n. In slow files, MFPT L3 (in the number of jumps). We explain these valuable results with various methods and approaches, e.g., we derive a general mapping from the mean square displacement scaling law to the MFPT scaling law. We also connect the results with real life activities. Special Issue Comments: Mean first passage scaling law in single file dynamics and various particular results in files are derived in this project. The project is related to the Special Issue projects about heterogeneous files and slow files,27 expansions in files,26 files with force32 and the first passage time in files.23 © 2016 World Scientific Publishing Company.

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