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Robert Hołyst

Publications and source records attributed to Robert Hołyst.

13 recordsLinked to original sources
arXiv2026

smICA: Open-Source Software for Quantitative, Lifetime-Resolved Mapping of Absolute Fluorophore Concentrations in Living Cells

Advanced microscopy techniques are essential in biomedical research for visualising and tracking biomolecules within living cells and their compartments. Conventional fluorescence microscopy methods, however, often struggle with accurately measuring the absolute concentrations of fluorescent probes in living cells. To overcome these limitations, we introduce an open-source analysis tool, smICA (Single-Molecule Image to Concentration Analyser). The smICA method offers quantitative mapping of absolute fluorophore concentrations, lifetime-resolved filtering methods of the signal, intensity-based cell segmentation, and requires only a few photons per pixel. Our approach also reduces the time required to determine the mean concentration per cell compared to the standard FCS measurement performed in multiple posts. To highlight the robustness of the method, we validated it against standard fluorescence correlation spectroscopy (FCS) measurements by performing in vitro (polymers in aqueous solution) and in vivo (polymers and EGFP in living cells) experiments. Finally, we present exemplary studies on the time evolution of fluorescently labelled mRNA concentration in living cells. The presented methodology, along with the software, is a promising tool for quantitative single-cell studies, including, but not limited to, protein expression, biomolecule degradation (such as proteins and mRNA), and monitoring enzymatic reactions.

q-bio.QM↗
arXiv2025

Global non-equilibrium thermodynamics of stationary states applied to the Rayleigh-Bénard convection

Classical thermodynamics describes physical systems in thermodynamic equilibrium, characterized in particular by the absence of macroscopic motion. Global non-equilibrium thermodynamics extends this framework to include physical systems in stationary states (Hołyst et al., EPL 149, 30001 (2025)). Here, we demonstrate that this extended theory captures macroscopic motion in stationary states, thereby providing a unified framework for global thermodynamics and fluid mechanics. We apply the theory to stationary Rayleigh-Bénard convection and show how the second law of global non-equilibrium thermodynamics determines the direction of changes in fluid motion.

physics.flu-dyn↗
arXiv2025

Brownian motion at various length scales with hydrodynamic and direct interactions

Brownian motion is essential for describing diffusion in systems ranging from simple to complex liquids. Unlike simple liquids, which consist of only a solvent, complex liquids, such as colloidal suspensions or the cytoplasm of a cell, are mixtures of various constituents with different shapes and sizes. Describing Brownian motion in such multiscale systems is extremely challenging because direct and many-body hydrodynamic interactions (and their interplay) play a pivotal role. Diffusion of small particles is mainly governed by a low viscous character of the solution, whereas large particles experience a highly viscous flow of the complex liquid on the macro scale. A quantity that encodes hydrodynamics on both length scales is the wave-vector-dependent viscosity. Assuming this quantity to be known -- in contrast to most studies in which the solvent shear viscosity is given -- provides a new perspective on studying the diffusivity of a tracer, especially in situations where the tracer size can vary by several orders of magnitude. Here, we start systematic studies of exact formal microscopic expressions for the short- and long-time self-diffusion coefficients of a single probe particle in a complex liquid in terms of short-ranged hydrodynamic response kernels. We study Brownian motion as a function of the probe size, contrasting most theories that focus on self-diffusion as a function of the crowder volume fraction. We discuss the limits of small and large probe sizes for various levels of approximations in our theory, and discuss the current successes and shortcomings of our approach.

cond-mat.soft↗
arXiv2024

Direction of spontaneous processes in non-equilibrium systems with movable/permeable internal walls

The second law of equilibrium thermodynamics explains the direction of spontaneous processes in a system after removing internal constraints. When the system only exchanges energy with the environment as heat, the second law states that spontaneous processes at constant temperature satisfy: $\textrm{d} U - δQ \leq 0$. Here, $\textrm{d} U$ is the infinitesimal change of the internal energy, and $δQ$ is the infinitesimal heat exchanged in the process. We will consider three different systems in a heat flow: ideal gas, van der Waals gas, and a binary mixture of ideal gases. We will also study ideal gas and van der Waals gas in the heat flow and gravitational field. We will divide each system internally into two subsystems by a movable wall. We will show that the direction of the motion of the wall, after release, at constant boundary conditions is determined by the same inequality as in equilibrium thermodynamics. The only difference between equilibrium and non-equilibrium law is the dependence of the net heat change, $δQ$, on the state parameters of the system. We will also consider a wall thick and permeable to gas particles and derive Archimedes' principle in the heat flow. Finally, we will study the ideal gas's Couette flow, where the direction of the motion of the internal wall follows from the inequality $\textrm{d} E - δQ - δW_s \leq 0$, with $\textrm{d} E$ being the infinitesimal change of the total energy (internal and kinetic) and $δW_s$ the infinitesimal work exchanged with the environment due to shear force. Ultimately, we will synthesize all these cases in a framework of the second law of non-equilibrium thermodynamics.

cond-mat.stat-mech↗
arXiv2024

The first law of thermodynamics in hydrodynamic steady and unsteady flows

We studied planar compressible flows of ideal gas as models of a non-equilibrium thermodynamic system. We demonstrate that internal energy $U(S^{*},V,N)$ of such systems in stationary and non-stationary states is the function of only three parameters of state, i.e. non-equilibrium entropy $S^{*}$, volume $V$ and number of particles $N$ in the system. Upon transition between different states, the system obeys the first thermodynamic law, i.e. $dU=T^{*}dS^{*}-p^{*}dV+μ^{*}dN$, where $U=3/2 NRT^{*}$ and $p^{*}V=NRT^{*}$. Placing a cylinder inside the channel, we find that U depends on the location of the cylinder $y_{c}$ only via the parameters of state, i.e. $U(S^{*}(y_{c}),V,N(y_{c}))$ at V=const. Moreover, when the flow around the cylinder becomes unstable, and velocity, pressure, and density start to oscillate as a function of time, t, U depends on t only via the parameters of state, i.e. $U(S^{*}(t),V,N(t))$ for V=const. These examples show that such a form of internal energy is robust and does not depend on the particular boundary conditions even in the unsteady flow.

cond-mat.stat-mech↗
arXiv2023

Steady state thermodynamics of ideal gas in shear flow

Equilibrium thermodynamics describes the energy exchange of a body with its environment. Here, we describe the global energy exchange of an ideal gas in the Coutte flow in a thermodynamic-like manner. We derive a fundamental relation between internal energy as a function of parameters of state. We analyze a non-equilibrium transition in the system and postulate the extremum principle, which determines stable stationary states in the system. The steady-state thermodynamic framework resembles equilibrium thermodynamics.

cond-mat.stat-mech↗
arXiv2023

Steady thermodynamic fundamental relation for the interacting system in a heat flow

There is a long-standing question of whether it is possible to extend the formalism of equilibrium thermodynamics to the case of non-equilibrium systems in steady states. We have made such an extension for an ideal gas in a heat flow [Hołyst \emph{et al.}, J. Chem. Phys. 157, 194108 (2022)]. Here we investigate whether such a description exists for the system with interactions: the Van der Waals gas in a heat flow. We introduce the parameters of state, each associated with a single way of changing energy. The first law of non-equilibrium thermodynamics follows from these parameters. The internal energy $U$ for the non-equilibrium states has the same form as in equilibrium thermodynamics. For the Van der Waals gas, $U(S^*, V, N, a^*,b^* )$ is a function of only 5 parameters of state (irrespective of the number of parameters characterizing the boundary conditions): the entropy $S^*$, volume $V$, number of particles $N$, and the rescaled Van der Waals parameters $a^*$, $b^*$. The state parameters, $a^*$, $b^*$, together with $S^*$, determine the net heat exchange with the environment.

cond-mat.stat-mech↗
arXiv2022

Thermodynamics of stationary states of the ideal gas in a heat flow

There is a long-standing question as to whether and to what extent it is possible to describe nonequilibrium systems in stationary states in terms of global thermodynamic functions. The positive answers have been obtained only for isothermal systems or systems with small temperature differences. We formulate thermodynamics of the stationary states of the ideal gas subjected to heat flow in the form of the zeroth, first, and second law. Surprisingly, the formal structure of steady state thermodynamics is the same as in equilibrium thermodynamics. We rigorously show that $U$ satisfies the following equation $dU=T^{*}dS^{*}-pdV$ for a constant number of particles, irrespective of the shape of the container, boundary conditions, size of the system, or mode of heat transfer into the system. We calculate $S^{*}$ and $T^{*}$ explicitly. The theory selects stable nonequilibrium steady states in a multistable system of ideal gas subjected to volumetric heating. It reduces to equilibrium thermodynamics when heat flux goes to zero.

cond-mat.stat-mech↗
arXiv2020

Storage of energy in constrained non-equilibrium systems

We study a quantity $\mathcal{T}$ defined as the energy U, stored in non-equilibrium steady states (NESS) over its value in equilibrium $U_0$, $ΔU=U-U_0$ divided by the heat flow $J_{U}$ going out of the system. A recent study suggests that $\mathcal{T}$ is minimized in steady states (Phys.Rev.E.99, 042118 (2019)). We evaluate this hypothesis using an ideal gas system with three methods of energy delivery: from a uniformly distributed energy source, from an external heat flow through the surface, and from an external matter flow. By introducing internal constraints into the system, we determine $\mathcal{T}$ with and without constraints and find that $\mathcal{T}$ is the smallest for unconstrained NESS. We find that the form of the internal energy in the studied NESS follows $U=U_0*f(J_U)$. In this context, we discuss natural variables for NESS, define the embedded energy (an analog of Helmholtz free energy for NESS), and provide its interpretation.

cond-mat.stat-mech↗
arXiv2020

Energy Storage in Steady States under Cyclic Local Energy Input

We study periodic steady states of a lattice system under external cyclic energy supply using simulation. We consider different protocols for cyclic energy supply and examine the energy storage. Under the same energy flux, we found that the stored energy depends on the details of the supply, period and amplitude of the supply. Further, we introduce an adiabatic wall as internal constrain into the lattice and examine the stored energy with respect to different positions of the internal constrain. We found that the stored energy for constrained systems are larger than their unconstrained counterpart. We also observe that the system stores more energy through large and rare energy delivery, comparing to small and frequent delivery.

cond-mat.stat-mech↗
arXiv2019

Flux and storage of energy in non-equilibrium, stationary states

Systems kept out of equilibrium in stationary states by an external source of energy store an energy $ΔU=U-U_0$. $U_0$ is the internal energy at equilibrium state, obtained after the shutdown of energy input. We determine $ΔU$ for two model systems: ideal gas and Lennard-Jones fluid. $ΔU$ depends not only on the total energy flux, $J_U$, but also on the mode of energy transfer into the system. We use three different modes of energy transfer where: the energy flux per unit volume is (i) constant; (ii) proportional to the local temperature (iii) proportional to the local density. We show that $ΔU /J_U=τ$ is minimized in the stationary states formed in these systems, irrespective of the mode of energy transfer. $τ$ is the characteristic time scale of energy outflow from the system immediately after the shutdown of energy flux. We prove that $τ$ is minimized in stable states of the Rayleigh-Benard cell.

cond-mat.stat-mech↗
arXiv1995

Polydispersity and ordered phases in solutions of rodlike macromolecules

We apply density functional theory to study the influence of polydispersity on the stability of columnar, smectic and solid ordering in the solutions of rodlike macromolecules. For sufficiently large length polydispersity (standard deviation $σ>0.25$) a direct first-order nematic-columnar transition is found, while for smaller $σ$ there is a continuous nematic-smectic and first-order smectic-columnar transition. For increasing polydispersity the columnar structure is stabilized with respect to solid perturbations. The length distribution of macromolecules changes neither at the nematic-smectic nor at the nematic-columnar transition, but it does change at the smectic-columnar phase transition. We also study the phase behaviour of binary mixtures, in which the nematic-smectic transition is again found to be continuous. Demixing according to rod length in the smectic phase is always preempted by transitions to solid or columnar ordering.

cond-mat↗