arXiv subjects

Jordane Preto

Publications and source records attributed to Jordane Preto.

9 recordsLinked to original sources

arXiv2026

Hamiltonian model for energy condensation in classical systems: Relevance to proteins

Recent experimental evidence for collective protein vibrations in the terahertz (THz) domain indicates that energy in biomolecular systems can self-organize in an orderly manner, as anticipated by Fröhlich's theory of condensates within a quantum framework. As a first step to bridge THz experiments with theory, we study the Hamiltonian dynamics of a classical network of coupled normal modes representing Fröhlich-type systems. Our results demonstrate that biologically relevant condensates can emerge at room temperature under appropriate nonlinear coupling schemes. The condensation mechanism remains robust also when the original Fröhlich resonance conditions are relaxed.

physics.bio-ph↗

arXiv2019

On the capacitive properties of individual microtubules and their meshworks

Microtubules are hollow cylindrical polymers composed of the highly negatively-charged (~23e), high dipole moment (1750 D) protein a,b-tubulin. While the roles of microtubules in chromosomal segregation, macromolecular transport and cell migration are relatively well-understood, studies on the electrical properties of microtubules have only recently gained strong interest. Here, we show that while microtubules at physiological concentrations increase solution capacitance, free tubulin has no appreciable effect. For a particular microtubule concentration, we were able to quantify these effects by determining the capacitance and resistance of a single 20 um-long microtubule to be 1.86 x 10^(-12) F and 1.07 x 10^12 Ohms respectively. Further, we observed a decrease in electrical resistance of solution, with charge transport peaking between 20-60 Hz in the presence of microtubules, consistent with recent findings that microtubules exhibit electric oscillations at such low frequencies. Our results show that in addition to macromolecular transport, microtubules also act as charge-storage devices through counterionic condensation across a broad frequency spectrum. We conclude with a hypothesis of an electrically-tunable cytoskeleton where the dielectric properties of tubulin are polymerization-state dependent.

physics.bio-ph↗

arXiv2018

Out-of-equilibrium collective oscillation as phonon condensation in a model protein

In the first part of the present paper (theoretical), the activation of out-of-equilibrium collective oscillations of a macromolecule is described as a classical phonon condensation phenomenon. If a macromolecule is modeled as an open system, that is, it is subjected to an external energy supply and is in contact with a thermal bath to dissipate the excess energy, the internal nonlinear couplings among the normal modes make the system undergo a non-equilibrium phase transition when the energy input rate exceeds a threshold value. This transition takes place between a state where the energy is incoherently distributed among the normal modes, to a state where the input energy is channeled into the lowest frequency mode entailing a coherent oscillation of the entire molecule. The model put forward in the present work is derived as the classical counterpart of a quantum model proposed long time ago by H. Fröhlich in the attempt to explain the huge speed of enzymatic reactions. In the second part of the present paper (experimental), we show that such a phenomenon is actually possible. Two different and complementary THz near-field spectroscopic techniques, a plasmonic rectenna, and a micro-wire near-field probe, have been used in two different labs to get rid of artefacts. By considering a aqueous solution of a model protein, the BSA (Bovine Serum Albumin), we found that this protein displays a remarkable absorption feature around 0.314 THz, when driven in a stationary out-of-thermal equilibrium state by means of optical pumping. The experimental outcomes are in very good qualitative agreement with the theory developed in the first part, and in excellent quantitative agreement with a theoretical result allowing to identify the observed spectral feature with a collective oscillation of the entire molecule.

cond-mat.soft↗

arXiv2017

Detection of long-range electrostatic interactions between charged molecules by means of Fluorescence Correlation Spectroscopy

The present paper deals with an experimental feasibility study concerning the detection of long- range intermolecular interactions through molecular diffusion behavior in solution. This follows previous analyses, theoretical and numerical, where it was found that inter-biomolecular long-range force fields of electrodynamic origin could be detected through deviations from Brownian diffusion. The suggested experimental technique was Fluorescence Correlation Spectroscopy (FCS). By con- sidering two oppositely charged molecular species in watery solution, that is, Lysozyme protein and a fluorescent dye molecule (Alexa488), the diffusion coefficient of the dye has been measured by means of the FCS technique at different values of the concentration of Lysozyme molecules, that is, at different average distances between the oppositely charged molecules. For the model consid- ered long-range interactions are built-in as electrostatic forces, the action radius of which can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular Dynamics simulations provide a clear and unambiguous interpretation of the experimental results.

physics.bio-ph↗

arXiv2014

On the role of electrodynamic interactions in long-distance biomolecular recognition

The issue of retarded long-range resonant interactions between two molecules with oscillating dipole moments is reinvestigated within the framework of classical electrodynamics. By taking advantage of a theorem in complex analysis, we present a simple method to calculate the frequencies of the normal modes, which are then used to estimate the interaction potential. The main results thus found are in perfect agreement with several results obtained from quantum computations. Moreover, when applied in a biophysical context, our findings shed new light on Frohlich's theory of selective long-range interactions between biomolecules. In particular, at variance with a long-standing belief, we show that sizable resonant long-range interactions may exist only if the interacting system is out of thermal equilibrium.

physics.bio-ph↗

arXiv2014

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: Numerical study

The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is shown that when the particles are uniformly distributed throughout the accessible space, the self-diffusion coefficient is always lowered by the considered interparticle interactions, irrespective of their attractive or repulsive character. This fact is also confirmed by a simple model to compute the correction to the Brownian diffusion coefficient due to the interactions among the particles. These interactions are also responsible for the onset of dynamical chaos and an associated chaotic diffusion which still follows an Einstein-Fick like law for the mean square displacement as a function of time. Transitional phenomena are observed for Coulomb-electrostatic (repulsive) and dipole-electrodynamic (attractive) interactions considered both separately and in competition. The outcomes reported in this paper clearly indicate a feasible experimental method to probe the activation of resonant electrodynamic interactions among biomolecules.

physics.bio-ph↗

arXiv2012

Semi-classical statistical approach to Fröhlich condensation theory

Fröhlich model equations describing phonon condensation in open systems of biological relevance are here reinvestigated in a semi-classical non-equilibrium statistical context (with "semi-classical" it is meant that the evolution of the system is described by means of classical equations with the addition of energy quantization). In particular, the assumptions that are necessary to deduce Fröhlich rate equations are highlighted and we show how these hypotheses led us to write an appropriate form for the master equation. As a comparison with known previous results, analytical relations with the Wu-Austin quantum Hamiltonian description are emphasized. Finally, we show how solutions of the master equation can be implemented numerically and outline some representative results of the condensation effect. Our approach thus provides more information with respect to the existing ones, in what we are concerned with the time evolution of the probability density functions instead of following average quantities.

physics.bio-ph↗

arXiv2012

Long-range resonant interactions in biological systems

The issue of retarded long-range resonant interactions between two molecules with oscillating dipole moments is reinvestigated within the framework of classical electrodynamics. By taking advantage of a theorem in complex analysis, we present a simple method to work out the frequencies of the normal modes, which are then used to estimate the interaction potential. The main results thus found are in perfect agreement with several outcomes obtained from quantum computations. Moreover, when applied to a biophysical context, our findings shed new light on Fröhlich's theory of selective long-range interactions between biomolecules. In particular, at variance with a long-standing belief, we show that sizable resonant long-range interactions may exist only if the interacting system is out of thermal equilibrium.

physics.bio-ph↗

arXiv2012

Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis

Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in the living matter. That such an exquisite level of accuracy may result from encountering forces solely driven by thermal diffusive processes is unlikely. Here we propose a yet unexplored strategy to experimentally tackle the long-standing question of a possibly active recruitment at a distance of cognate partners of biomolecular reactions via the action of resonant electrodynamic interactions. We considered two simplified models for a preliminary feasibility investigation of the devised methodology. By taking advantage of advanced experimental techniques nowadays available, we propose to measure the characteristic encounter time scales of dually-interacting biopartners and to compare them with theoretical predictions worked out both in the presence or absence of putative long-range electromagnetic forces.

physics.bio-ph↗