arXiv subjects

John Palmeri

Publications and source records attributed to John Palmeri.

At least 19 recordsLinked to original sources

arXiv2026

Equilibrium cluster statistics of cooperative and anticooperative binding on finite one-dimensional rings

We study equilibrium clustering in a finite one-dimensional lattice gas of $L$ sites with periodic boundary conditions, as a minimal model for adsorption and binding on small ring-like substrates. Using a grand-canonical formulation with nearest-neighbor coupling, we derive exact finite-size expressions for the mean occupancy, the mean number of domain walls, and the mean number of clusters. Building on exact $k$-site correlation functions, we further derive expressions for the mean number of clusters of size $k$ and for two complementary size statistics: the cluster-size distribution, and the site-weighted cluster-size distribution. These observables characterize how spatial organization changes across attractive (cooperative) and repulsive (anticooperative) interactions, and highlight finite-size and parity-dependent effects of the underlying lattice, the latter being particularly pronounced near half filling in small systems. To access larger lattices without enumerating all $2^L$ microstates, we also develop a cluster-based combinatorial formulation in which configurations are classified by cluster counts and sizes, reducing the effective state space to a set whose size scales with integer partitions, $\approx e^{\sqrt{L}}$, rather than with $\approx e^{L}$. Taken together, our results provide exact benchmarks for finite periodic systems and suggest experimentally relevant cluster observables that complement occupancy-based measures of cooperativity, with particular relevance for binding on ring-like substrates for biological assemblies.

cond-mat.stat-mech↗

arXiv2024

Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor

The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and the residence time in an occupancy state. Since the relative standard deviation from the statistical mean monotonically decreases with the number of binding sites, these techniques are only suitable for small enough systems, such as those implicated in stochastic processes inside cells. Here, we present a general-purpose grand canonical Hamiltonian description of a small one-dimensional (1D) lattice gas with either nearest-neighbor or long-range interactions as prototypical examples of cooperativity-influenced adsorption processes. First, we elucidate how the strength and sign of the interaction potential between neighboring bound particles on the lattice determine the intensity of the fluctuations of the mean occupancy. We then employ this relationship to compare the theoretical predictions of our model to data from single molecule experiments on bacterial flagellar motors (BFM) of E. coli. In this way, we find evidence that cooperativity controls the mechano-sensitive dynamical assembly of the torque-generating units, the so-called stator units, onto the BFM. Furthermore, in an attempt to quantify fluctuations and the adaptability of the BFM, we estimate the stator-stator interaction potential. Finally, we conclude that the system resides in a sweet spot of the parameter space (phase diagram) suitable for a smoothly adaptive system while minimizing fluctuations.

physics.bio-ph↗

arXiv2023

Chain decay and rates disorder in the totally asymmetric simple exclusion process

We theoretically study the Totally Asymmetric Exclusion Process (TASEP) with quenched jumping rates disorder and finite lifetime chain. TASEP is widely used to model the translation of messenger RNAs by Ribosomes in protein synthesis. Since the exact solution of the TASEP model is analytically and computationally intractable for biologically relevant systems parameters, the canonical Mean-Field (MF) approaches of solving coupled non-linear differential equations is also computational expensive for the scale of relevant biological data analysis. In this article, we provide alternative approach to computing the MF steady state solution via a computationally efficient system of non-linear algebraic equations. We further outline a framework for including correlations progressively via the exact solution of small size TASEP system. Leading order approximation in the biologically relevant entry rate limited regime shows remarkable agreement with the full Monte-Carlo simulation result for a wide range of system parameter space. These results could be of importance to the kinetic rates inference in Ribo-Seq data analysis and other related problems.

cond-mat.stat-mech↗

arXiv2023

Quantum capacitance governs electrolyte conductivity in carbon nanotubes

In recent experiments, unprecedentedly large values for the conductivity of electrolytes through carbon nanotubes (CNTs) have been measured, possibly owing to flow slip and a high pore surface charge density whose origin is still unknown. By accounting for the coupling between the {quantum} CNT and the {classical} electrolyte-filled pore capacitances, we study the case where a gate voltage is applied to the CNT. The computed surface charge and conductivity dependence on reservoir salt concentration and gate voltage are intimately connected to the CNT electronic density of states. This approach provides key insight into why metallic CNTs have larger conductivities than semi-conducting ones.

cond-mat.soft↗

arXiv2022

Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

physics.bio-ph↗

arXiv2021

Competition between Born solvation, dielectric exclusion, and Coulomb attraction in spherical nanopores

The recent measurement of a very low dielectric constant, $ε$, of water confined in nanometric slit pores leads us to reconsider the physical basis of ion partitioning into nanopores. For confined ions in chemical equilibrium with a bulk of dielectric constant $ε_b>ε$, three physical mechanisms, at the origin of ion exclusion in nanopores, are expected to be modified due to this dielectric mismatch: dielectric exclusion at the water-pore interface (with membrane dielectric constant, $ε_m<ε$), the solvation energy related to the difference in Debye-Hückel screening parameters in the pore, $κ$, and in the bulk $κ_b$, and the classical Born solvation self-energy proportional to $ε^{-1}-ε_b^{-1}$. Our goal is to clarify the interplay between these three mechanisms and investigate the role played by the Born contribution in ionic liquid-vapor (LV) phase separation in confined geometries. We first compute analytically the potential of mean force (PMF) of an ion of radius $R_i$ located at the center of a nanometric spherical pore of radius $R$. Computing the variational grand potential for a solution of confined ions, we then deduce the partition coefficients of ions in the pore. Phase diagrams of the LV transition are established for various parameter values and we show that a signature of this phase transition can be detected by monitoring the total osmotic pressure. For charged nanopores, these exclusion effects compete with the electrostatic attraction that imposes the entry of counterions into the pore to enforce electro-neutrality. This study will therefore help in deciphering the respective roles of the Born self-energy and dielectric mismatch in experiments and simulations of ionic transport through nanopores.

cond-mat.soft↗

arXiv2020

Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling

We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $σ$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.

physics.bio-ph↗

arXiv2018

Role of charge regulation and flow slip on the ionic conductance of nanopores: an analytical approach

The number of precise conductance measurements in nanopores is quickly growing. In order to clarify the dominant mechanisms at play and facilitate the characterization of such systems for which there is still no clear consensus, we propose an analytical approach to the ionic conductance in nanopores that takes into account (i) electro-osmotic effects, (ii) flow slip at the pore surface for hydrophobic nanopores, (iii) a component of the surface charge density that is modulated by the reservoir $p$H and salt concentration $c_s$ using a simple charge regulation model, and (iv) a fixed surface charge density that is unaffected by $p$H and $c_s$. Limiting cases are explored for various ranges of salt concentration and our formula is used to fit conductance experiments found in the literature for carbon nanotubes. This approach permits us to catalog the different possible transport regimes and propose an explanation for the wide variety of currently known experimental behavior for the conductance versus $c_s$.

cond-mat.soft↗

arXiv2017

Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

physics.bio-ph↗

arXiv2017

Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or "volumetric" chemophoresis, force field. This minimal description, in the sense of Occam's Razor principle, captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insights into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes.

q-bio.SC↗

arXiv2016

A variational approach to the liquid-vapor phase transition for hardcore ions in the bulk and in nanopores

We employ a field-theoretical variational approach to study the behavior of ionic solutions in the grand canonical ensemble. To describe properly the hardcore interactions between ions, we use a cutoff in Fourier space for the electrostatic contribution of the grand potential and the Carnahan-Starling equation of state with a modified chemical potential for the pressure one. We first calibrate our method by comparing its predictions at room temperature with Monte Carlo results for excess chemical potential and energy. We then validate our approach in the bulk phase by describing the classical "ionic liquid-vapor" phase transition induced by ionic correlations at low temperature, before applying it to electrolytes at room temperature confined to nanopores embedded in a low dielectric medium and coupled to an external reservoir of ions. The ionic concentration in the nanopore is then correctly described from very low bulk concentrations, where dielectric exclusion shifts the transition up to room temperature for sufficiently tight nanopores, to high concentrations where hardcore interactions dominate which, as expected, modify only slightly this ionic "capillary evaporation".

cond-mat.soft↗

arXiv2015

Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation

Fundamental understanding of ionic transport at the nanoscale is essential for developing biosensors based on nanopore technology and new generation high-performance nanofiltration membranes for separation and purification applications. We study here ionic transport through single putatively neutral hydrophobic nanopores with high aspect ratio (of length L=6 μm with diameters ranging from 1 to 10 nm) and with a well controlled cylindrical geometry. We develop a detailed hybrid mesoscopic theoretical approach for the electrolyte conductivity inside nanopores, which considers explicitly ion advection by electro-osmotic flow and possible flow slip at the pore surface. By fitting the experimental conductance data we show that for nanopore diameters greater than 4 nm a constant weak surface charge density of about 10$^{-2}$ C m$^{-2}$ needs to be incorporated in the model to account for conductance plateaus of a few pico-Siemens at low salt concentrations. For tighter nanopores, our analysis leads to a higher surface charge density, which can be attributed to a modification of ion solvation structure close to the pore surface, as observed in the molecular dynamics simulations we performed.

cond-mat.mes-hall↗

arXiv2013

Slow closure of denaturation bubbles in DNA: twist matters

The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $κ_ϕ=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $κ_ϕ$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.

cond-mat.soft↗

arXiv2013

The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation

The interface between the vapor and liquid phase of quadrupolar-dipolar fluids is the seat of an electric interfacial potential whose influence on ion solvation and distribution is not yet fully understood. To obtain further microscopic insight into water specificity we first present extensive classical molecular dynamics simulations of a series of model liquids with variable molecular quadrupole moments that interpolates between SPC/E water and a purely dipolar liquid. We then pinpoint the essential role played by the competing multipolar contributions to the vapor-liquid and the solute-liquid interface potentials in determining an important ion-specific direct electrostatic contribution to the ionic solvation free energy for SPC/E water---dominated by the quadrupolar and dipolar contributions---beyond the dominant polarization one. Our results show that the influence of the vapor-liquid interfacial potential on ion solvation is strongly reduced due to the strong partial cancellation brought about by the competing solute-liquid interface potential.

cond-mat.soft↗

arXiv2012

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $λ$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.

cond-mat.soft↗

arXiv2012

Strand diffusion-limited closure of denaturation bubbles in DNA

The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a bending modulus which depends on the base-pair state, with double-strand DNA (dsDNA) segments being 50 times stiffer than ssDNA ones. For DNA lengths from N=20 to 100 base-pairs (bp) and initial bubble sizes of N-6 bp, long closure times of 0.1 to 4 microseconds are found, following a scaling law in N^2.4. The bubble starts to close by a fast zipping which stops when the bubble reaches a highly bent metastable state of length around 10 bp. The limiting final step to complete closure is controlled by the dsDNA "arms" rotational diffusion, with closure occurring once they are nearly aligned. The central role of chain bending, which cannot be accounted for in one-dimensional models, is thus illuminated.

cond-mat.soft↗

arXiv2011

Ionic exclusion phase transition in neutral and weakly charged cylindrical nanopores

A field theoretic variational approach is introduced to study ion penetration into water-filled cylindrical nanopores in equilibrium with a bulk reservoir. It is shown that (i) an ion located in a neutral pore undergoes two opposing mechanisms: the deformation of its surrounding ionic cloud of opposite charge, with respect to the reservoir, which increases the surface tension and tends to exclude ions form the pore, and (ii) the attractive contribution to the ion self-energy of the repulsive image forces associated with the dielectric jump between the solvent and the pore wall, which becomes more and more screened when ions enter the pore. For pore radii around 1 nm and bulk concentrations lower than 0.2 mol/L, this mechanism leads to a first-order phase transition, similar to capillary "evaporation", from an ionic-penetration state to an ionic-exclusion state. The discontinuous phase transition survives within the biological concentration range (~ 0.15 mol/L) for small enough membrane dielectric permittivities (< 5). In the case of a weakly charged pore, counterion penetration exhibits a non-monotonic behaviour and is characterized by two regimes: at low reservoir concentration or small pore radii, coions are excluded and the energy barrier for counterions is reduced but image forces remain strong enough, so that the counterion partition coefficient in the pore decreases with increasing reservoir concentration up to a characteristic value; for larger reservoir concentrations, image forces are screened and the partition coefficient of counterions increases with the reservoir electrolyte concentration.

cond-mat.soft↗

arXiv2010

Ionic Capillary Evaporation in Weakly Charged Nanopores

Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration "liquid" phase to an ionic-exclusion "vapor" phase, controlled by nanopore-modified ionic correlations and dielectric repulsion. For weakly charged nanopores, this pseudotransition survives and may shed light on the mechanism behind the rapid switching of nanopore conductivity observed in experiments.

cond-mat.soft↗