arXiv subjects

Ralf Blossey

Publications and source records attributed to Ralf Blossey.

At least 19 recordsLinked to original sources

arXiv2026

Quantum Thermodynamics of Electron Transport along Chains of Redox Centers

Intramolecular electron transport in biological systems is typically described as a diffusive hopping process, according to the semi-classical rate theories of Marcus and Hopfield combined with classical Pauli-type master equations. However, the possibility that non-trivial quantum mechanical effects could play a functional role in the transport dynamics in certain biomolecular processes has attracted increasing attention. Here, we extend the quantum mechanical model of open system dynamics by the Lindblad equation to a key biological component, the long chains of redox centers based on iron-sulfur clusters or heme groups that are widespread in many biological organisms, where they realize the cellular respiration. This approach allows to explore a wide range of physical parameters, showing key features of electron transport in these multi-domain protein structures. We pay particular attention to heat and entropy transfer between the electrons and the protein bath, which constitutes a benchmark of physical realism for the models. Electron currents, average transfer times and relative efficiency of the transport process are also explicitly characterized.

physics.chem-ph↗

arXiv2026

A trick of the tail: how electrostatics helps a DNA repair enzyme to localize on nucleosomes

Electrostatic interactions are key to the recognition processes of proteins and DNA and have been previously documented for the action of repair enzymes. Uracil-DNA glycosylase (UDG) is the first in a sequence of enzymes that act in the base-excision repair process (BER) and whose task is the extraction of uracil bases from nuclear DNA. The question of how the molecule targets uracil bases in chromatin, in particular in the condensed protein-DNA complexes of nucleosomes, has only recently become a subject of detailed studies. Here we show that the presence of an arginine anchor motif on the N-terminal tail of UDG can favor its localization on nucleosomes by binding to their acidic patches on their top and bottom surfaces via electrostatic interactions. We argue that this mechanism can play a key role in the detection of uracil defects in nucleosomal DNA.

cond-mat.soft↗

arXiv2026

Boltzmann to Lindblad: Classical and Quantum Approaches to Out-of-Equilibrium Statistical Mechanics

Open quantum systems play a central role in contemporary nanoscale technologies, including molecular electronics, quantum heat engines, quantum computation and information processing. A major theoretical challenge is to construct dynamical models that are simultaneously consistent with classical thermodynamics and complete positivity. In this work, we develop a framework that addresses this issue by extending classical stochastic dynamics to the quantum domain. We begin by formulating a generalized Langevin equation in which both friction and noise act symmetrically on the two Hamiltonian equations. From this, we derive a generalized Klein-Kramers equation expressed in terms of Poisson brackets, and we show that it admits the Boltzmann distribution as its stationary solution while satisfying the first and second laws of thermodynamics along individual trajectories. Applying canonical quantization to this classical framework yields two distinct quantum master equations, depending on whether the friction operators are taken to be Hermitian or non-Hermitian. By analyzing the dynamics of a harmonic oscillator, we determine the conditions under which these equations reduce to a Lindblad-type generator. Our results demonstrate that complete positivity is ensured only when friction and noise are included in both Hamiltonian equations, thus fully justifying the classical construction. Moreover, we find that the friction coefficients must satisfy the same positivity condition in both the Hermitian and non-Hermitian formulations, revealing a form of universality that transcends the specific operator representation. The formalism offers a versatile tool for deriving quantum versions of the thermodynamic laws and is directly applicable to a wide class of nonequilibrium nanoscale systems.

quant-ph↗

arXiv2025

Explicit noise and dissipation operators for quantum stochastic thermodynamics

The theory of open quantum systems plays a fundamental role in several scientific and technological disciplines, from quantum computing and information science to molecular electronics and quantum thermodynamics. Despite its widespread relevance, a rigorous formulation of quantum dissipation in conjunction with thermal noise remains a topic of active research. In this work, we establish a formal correspondence between classical stochastic thermodynamics, in particular the Fokker-Planck and Klein-Kramers equations, and the quantum master equation. Building on prior studies of multiplicative noise in classical stochastic differential equations, we demonstrate that thermal noise at the quantum level manifests as a multidimensional geometric stochastic process. By applying canonical quantization, we introduce a novel Hermitian dissipation operator that serves as a quantum analogue of classical viscous friction. This operator allows for a well-defined expression of heat exchange between a system and its environment, enabling the formulation of an alternative quantum equipartition theorem. Our framework ensures a precise energy balance that aligns with the first law of thermodynamics and an entropy balance consistent with the second law. The theoretical formalism is applied to two prototypical quantum systems, the harmonic oscillator and a particle in an infinite potential well, for which it provides new insights into nonequilibrium thermodynamics at the quantum scale. Our results advance the understanding of dissipation in quantum systems and establish a foundation for future studies on stochastic thermodynamics in the quantum domain.

quant-ph↗

arXiv2025

The diffusive dynamics and electrochemical regulation of weak polyelectrolytes across liquid interfaces

We propose a framework to study the spatio-temporal evolution of liquid-liquid phase separation of weak polyelectrolytes in ionic solutions. Unlike strong polyelectrolytes, which carry a fixed charge, the charge state of weak polyelectrolytes is modulated by the electrochemical environment through protonation and deprotonation processes. Leveraging numerical simulations and analysis, our work reveals how solution acidity (pH) influences the formation, interactions, and structural properties of phase-separated coacervates. We find that pH gradients can be maintained across coacervate interfaces resulting in a clear distinction in the electro-chemical properties within and outside the coacervate. By regulating the charge state of weak polyelectrolytes, pH gradients interact and modulate the electric double layer forming at coacervate interfaces eventually determining how they interact. Further linear and nonlinear analyses of stationary localised solutions reveal a rich spectrum of behaviours that significantly distinguish weak from strong polyelectrolytes. Overall, our results demonstrate the importance of charge regulation on phase-separating solutions of charge-bearing molecules and the possibility of harnessing charge-regulated mechanisms to control coacervates and shape their stability and spatial organisation.

cond-mat.soft↗

arXiv2025

Surface polarization strongly influences electrostatics in a nonlocal medium

Electrostatics in the solution phase is governed by free electrical charges such as ions, as well as by bound charges that arise when a polarizable medium responds to an applied field. In a local medium, described by a constant dielectric permittivity, the sign of the far-field electrostatic potential distribution around an object is governed by its electrical charge. We demonstrate significant departures from this expectation in a nonlocal medium characterized by a wave vector-dependent dielectric function. Here, surface polarization due to the solvent, or indeed non-solvent dipoles, may wield significant influence at large distances. The polarization correlation length may not only significantly augment the effective screening length, but we also show that the electrical contribution from polarization can compete with and even invert the sign of the electrical potential and the field arising from charge alone. These results hold ramifications for a range of apparently anomalous electrically governed observations such as underscreening, electrophoretic mobilities of charge-neutral objects, and long-ranged attraction between like-charged entities in water and other solvents.

cond-mat.soft↗

arXiv2024

The effective diffusion constant of stochastic processes with spatially periodic noise

We discuss the effective diffusion constant $D_{\it eff}$ for stochastic processes with spatially-dependent noise. Starting from a stochastic process given by a Langevin equation, different drift-diffusion equations can be derived depending on the choice of the discretization rule $ 0 \leq α\leq 1$. We initially study the case of periodic heterogeneous diffusion without drift and we determine a general result for the effective diffusion coefficient $D_{\it eff}$, which is valid for any value of $α$. We study the case of periodic sinusoidal diffusion in detail and we find a relationship with Legendre functions. Then, we derive $D_{\it eff}$ for general $α$ in the case of diffusion with periodic spatial noise and in the presence of a drift term, generalizing the Lifson-Jackson theorem. Our results are illustrated by analytical and numerical calculations on generic periodic choices for drift and diffusion terms.

cond-mat.stat-mech↗

arXiv2024

Short-time expansion of one-dimensional Fokker-Planck equations with heterogeneous diffusion

We formulate a short-time expansion for one-dimensional Fokker-Planck equations with spatially dependent diffusion coefficients, derived from stochastic processes with Gaussian white noise, for general values of the discretization parameter $0 \leq α\leq 1$ of the stochastic integral. The kernel of the Fokker-Planck equation (the propagator) can be expressed as a product of a singular and a regular term. While the singular term can be given in closed form, the regular term can be computed from a Taylor expansion whose coefficients obey simple ordinary differential equations. We illustrate the application of our approach with examples taken from statistical physics and biophysics. Further, we show how our formalism allows to define a class of stochastic equations which can be treated exactly. The convergence of the expansion cannot be guaranteed independently from the discretization parameter $α$.

physics.bio-ph↗

arXiv2023

Counterion-controlled phase equilibria in a charge-regulated polymer solution

We study phase equilibria in a minimal model of charge-regulated polymer solutions. Our model consists of a single polymer species whose charge state arises from protonation-deprotonation processes in the presence of a dissolved acid, whose anions serve as screening counterions. We explicitly account for variability in the polymers' charge states. Homogeneous equilibria in this model system are characterised by the total concentration of polymers, the concentration of counter-ions and the charge distributions of polymers which can be computed with the help of analytical approximations. We use these analytical results to characterise how parameter values and solution acidity influence equilibrium charge distributions and identify for which regimes uni-modal and multi-modal charge distributions arise. We then study the interplay between charge regulation, solution acidity and phase separation. We find that charge regulation has a significant impact on polymer solubility and allows for non-linear responses to the solution acidity: re-entrant phase behaviour is possible in response to increasing solution acidity. Moreover, we show that phase separation can yield to the coexistence of local environments characterised by different charge distributions and mixture compositions.

cond-mat.soft↗

arXiv2023

A comprehensive continuum theory of structured liquids

We develop a comprehensive continuum model capable of treating both electrostatic and structural interactions in liquid dielectrics. Starting from a two-order parameter description in terms of charge density and polarization, we derive a field-theoretic model generalizing previous theories. Our theory explicitly includes electrostatic and structural interactions in the bulk of the liquid and allows for polarization charges within a Drude model. In particular, we develop a detailed description of the boundary conditions which include the charge regulation mechanism and surface polarization. The general features for solving the saddle-point equations of our model are elucidated and future applications to predict and validate experimental results are outlined.

cond-mat.soft↗

arXiv2022

Infinite ergodicity for geometric Brownian motion

Geometric Brownian motion is an exemplary stochastic processes obeying multiplicative noise, with widespread applications in several fields, e.g. in finance, in physics and biology. The definition of the process depends crucially on the interpretation of the stochastic integrals which involves the discretization parameter $α$ with $0 \leq α\leq 1$ , giving rise to the well-known special cases $α=0$ (Itô), $α=1/2$ (Fisk-Stratonovich) and $α=1$ (Hänggi-Klimontovich or anti-Itô). In this paper we study the asymptotic limits of the probability distribution functions (PDFs) of geometric Brownian motion and some related generalizations. We establish the conditions for the existence of normalizable asymptotic distributions depending on the discretization parameter $α$. Using the infinite ergodicity approach, recently applied to stochastic processes with multiplicative noise by E. Barkai and collaborators, we show how meaningful asymptotic results can be formulated in a transparent way.

cond-mat.stat-mech↗

arXiv2022

A one-dimensional three-state run-and-tumble model with a `cell cycle'

We study a one-dimensional three-state run-and-tumble model motivated by the bacterium Caulobacter crescentus which displays a cell cycle between two non-proliferation mobile phase and a proliferating sedentary phase. Our model implements kinetic transitions between the two mobile and one sedentary states described in terms of their number densities, where mobility is allowed with different running speeds in forward and backward direction. We start by analyzing the stationary states of the system and compute the mean and squared-displacements for the distribution of all cells, as well as for the number density of settled cells. The latter displays a surprising super-ballistic scaling ~t^3 at early times. Including repulsive and attractive interactions between the mobile cell populations and the settled cells, we explore the stability of the system and then employ numerical methods to study structure formation in the fully nonlinear system. We find traveling waves of bacteria, whose occurrence is quantified in a nonequilibrium state diagram.

cond-mat.soft↗

arXiv2022

Continuum theories of structured dielectrics

Aequous dielectrics are ubiquitous in soft- and bio-nano matter systems. The theoretical description of such systems in terms of continuum (`macroscopic') theory remains a serious challenge. In this perspective we first review the existing continuum phenomenological approaches that have been developed in the past decades. In order to describe a path to advance continuum theory beyond these approaches we then take recourse to the Onsager-Dupuis theory of the dielectric behaviour of ice, which, for the case of a solid dielectric, exemplified important conceptual issues we deem relevant for the development of a more fundamental continuum theory of liquid dielectrics. Subsequently, we discuss our recently proposed continuum field theory of structured dielectrics, which provides a generalized approach to the dielectric behavior of such systems.

cond-mat.soft↗

arXiv2022

Field theory of structured liquid dielectrics

We develop of a field-theoretic approach for the treatment of both the non-local and the non-linear response of structured liquid dielectrics. Our systems of interest are composed of dipolar solvent molecules and simple salt cations and anions. We describe them by two independent order parameters, the polarization field for the solvent and the charge density field for the ions, including and treating the non-electrostatic part of the interactions explicitly and consistently. We show how to derive functionals for the polarization and the electrostatic field of increasingly finer scales and solve the resulting mean-field saddle-point equations in the linear regime. We derive criteria for the character of their solutions that depend on the structural lengths and the polarity of the solvent. Our approach provides a systematic way to derive generalized polarization theories.

cond-mat.soft↗

arXiv2022

Brownian particles driven by spatially periodic noise

We discuss the dynamics of a Brownian particle under the influence of a spatially periodic noise strength in one dimension using analytical theory and computer simulations. In the absence of a deterministic force, the Langevin equation can be integrated formally exactly. We determine the short- and long-time behaviour of the mean displacement (MD) and mean-squared displacement (MSD). In particular we find a very slow dynamics for the mean displacement, scaling as $t^{-1/2}$ with time $t$. Placed under an additional external periodic force near the critical tilt value we compute the stationary current obtained from the corresponding Fokker-Planck equation and identify an essential singularity if the minimum of the noise strength is zero. Finally, in order to further elucidate the effect of the random periodic driving on the diffusion process, we introduce a phase factor in the spatial noise with respect to the external periodic force and identify the value of the phase shift for which the random force exerts its strongest effect on the long-time drift velocity and diffusion coefficient.

cond-mat.stat-mech↗

arXiv2021

Active noise-driven particles under space-dependent friction in one dimension

We study a Langevin equation describing the stochastic motion of a particle in one dimension with coordinate $x$, which is simultaneously exposed to a space-dependent friction coefficient $γ(x)$, a confining potential $U(x)$ and non-equilibrium (i.e., active) noise. Specifically, we consider frictions $γ(x)=γ_0 + γ_1 | x |^p$ and potentials $U(x) \propto | x |^n$ with exponents $p = 1,2$ and $n = 0, 1, 2$. We provide analytical and numerical results for the particle dynamics for short times and the stationary probability density functions (PDFs) for long times. The short-time behaviour displays diffusive and ballistic regimes while the stationary PDFs display unique characteristic features depending on the exponent values $(p, n)$. The PDFs interpolate between Laplacian, Gaussian and bimodal distributions, whereby a change between these different behaviours can be achieved by a tuning of the friction strengths ratio $γ_0/γ_1$. Our model is relevant for molecular motors moving on a one-dimensional track and can also be realized for confined self-propelled colloidal particles.

cond-mat.soft↗

arXiv2020

Charge symmetry broken complex coacervation

Liquid-liquid phase separation has emerged as one of the important paradigms in the chemical physics as well as biophysics of charged macromolecular systems. We elucidate an equilibrium phase separation mechanism based on charge regulation, i.e., protonation-deprotonation equilibria controlled by pH, in an idealized macroion system which can serve as a proxy for simple coacervation. First, a low-density density-functional calculation reveals the dominance of two-particle configurations coupled by ion adsorption on neighboring macroions. Then a binary cell model, solved on the Debye-Hückel as well as the full nonlinear Poisson-Boltzmann level, unveils the charge-symmetry breaking as inducing the phase separation between low- and high-density phases as a function of pH. These results can be identified as a charge symmetry broken complex coacervation between chemically identical macroions.

cond-mat.soft↗

arXiv2019

Charge regulation radically modifies electrostatics in membrane stacks

Motivated by biological membrane-containing organelles in plants and photosynthetic bacteria, we study charge regulation in a model membrane stack. Considering (de)protonation as the simplest mechanism of charge equilibration between the membranes and with the bathing environment, we uncover a symmetry-broken charge state in the stack with a quasiperiodic effective charge sequence. In the case of a monovalent bathing salt solution our model predicts complex, inhomogeneous charge equilibria depending on the strength of the (de)protonation reaction, salt concentration, intermembrane separation, and their number in the stack. Our results shed light on the basic reorganization mechanism of thylakoid membrane stacks.

cond-mat.soft↗