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Radek Erban

Publications and source records attributed to Radek Erban.

At least 19 recordsLinked to original sources

Extended pseudo-spectral physics-informed neural networks for phase-field models

Phase-field models play a central role in the continuum description of phase separation, in which the bulk free-energy density and the interfacial thickness parameter determine pattern formation and microstructural evolution. In practice, these constitutive quantities are rarely known a priori and must be inferred from limited dynamical observations. In this work, an extended pseudo-spectral physics-informed neural network (ESPINN) framework is developed for the inverse identification of phase-field models from transient snapshot data. It enables the simultaneous recovery of both the bulk chemical potential and unknown gradient coefficients. Numerical experiments on the one-dimensional Cahn-Hilliard equation demonstrate accurate and statistically stable reconstruction in the noiseless regime, with substantial constitutive information recoverable from even a single snapshot pair. In the presence of noise, reconstruction accuracy degrades gracefully, and increasing the number of snapshots improves robustness by reducing variance across runs. These results establish ESPINN as a data-efficient and physically consistent approach for learning free-energy structure in continuum models of phase separation.

q-bio.QM

On the role of fractional Brownian motion in models of chemotaxis and stochastic gradient ascent

Cell migration often exhibits long-range temporal correlations and anomalous diffusion, even in the absence of external guidance cues such as chemical gradients or topographical constraints. This raises a fundamental question: do such correlations enhance a cell's ability to navigate complex environments? In this work, we explore how temporally correlated noise (modeled using fractional Brownian motion) influences chemotactic search dynamics. Through computational experiments, we show that superdiffusive motion, when combined with gradient-driven migration, enables robust exploration of the chemoattractant landscape. Cells reliably reach the global maximum of the concentration field, even in the presence of spatial noise, secondary cues, or irregular signal geometry. We quantify this behavior by analyzing the distribution of first hitting times under varying degrees of temporal correlation. Notably, our results are consistent across diverse conditions, including flat and curved substrates, and scenarios involving both primary and self-generated chemotactic signals. Beyond biological implications, these findings also offer insight into the design of optimization and sampling algorithms that benefit from structured stochasticity.

q-bio.QM

Impact of memory on clustering in spontaneous particle aggregation

The effect of short-term and long-term memory on spontaneous aggregation of organisms is investigated using a stochastic agent-based model. Each individual modulates the amplitude of its random motion according to the perceived local density of neighbors. Memory is introduced via a chain of $K$~internal variables that allow agents to retain information about previously encountered densities. The parameter $K$ controls the effective length of memory. A formal mean-field limit yields a macroscopic Fokker--Planck equation, which provides a continuum description of the system in the large-population limit. Steady states of this equation are characterized to interpret the emergence and morphology of clusters. Systematic stochastic simulations in one- and two-dimensional spatial domains reveal that short- or moderate-term memory promotes coarsening, resulting in a smaller number of larger clusters, whereas long-term memory inhibits aggregation and increases the proportion of isolated individuals. Statistical analysis demonstrates that extended memory reduces the agents' responsiveness to environmental stimuli, explaining the transition from aggregation to dispersion as $K$ increases. These findings identify memory as a key factor controlling the collective organization of self-driven agents and provide a bridge between individual-level dynamics and emergent spatial patterns.

math.DS

Neural networks for learning macroscopic chemotactic sensitivity from microscopic models

The macroscopic (population-level) dynamics of chemotactic cell movement -- arising from underlying microscopic (individual-based) models -- are often described by parabolic partial differential equations (PDEs) governing the spatio-temporal evolution of cell concentrations. In certain cases, these macroscopic PDEs can be analytically derived from microscopic models, thereby elucidating the dependence of PDE coefficients on the parameters of the underlying individual-based dynamics. However, such analytical derivations are not always feasible, particularly for more complex or nonlinear microscopic models. In these instances, neural networks offer a promising alternative for estimating the coefficients of macroscopic PDEs directly from data generated by microscopic simulations. In this work, three microscopic models of chemotaxis are investigated. The macroscopic chemotaxis sensitivity is estimated using neural networks, thereby bridging the gap between individual-level behaviours and population-level descriptions. The results are compared with macroscopic PDEs, which can be derived for each model in certain parameter regimes.

q-bio.QM

From Brownian dynamics to Poisson-Nernst-Planck equations: multi-resolution simulations of ions

Starting with a microscopic (individual-based) Brownian dynamics model of charged particles (ions), its macroscopic description is derived as a system of partial differential equations that govern the evolution of ion concentrations in space and time. The macroscopic equations are obtained in the form of the Poisson-Nernst-Planck system. A multi-resolution method for simulating charged particles is then developed, combining the detailed Brownian dynamics model in a part of the computational domain with coarser macroscopic equations in the remainder. The strengths, limitations, and applicability of microscopic, macroscopic, and multi-resolution simulation approaches are demonstrated through an illustrative model comprising a system of Na$^+$ and Cl$^-$ ions.

physics.comp-ph

Planar chemical reaction systems with algebraic and non-algebraic limit cycles

The Hilbert number $H(n)$ is defined as the maximum number of limit cycles of a planar autonomous system of ordinary differential equations (ODEs) with right-hand sides containing polynomials of degree at most $n \in {\mathbb N}$. The dynamics of chemical reaction systems with two chemical species can be (under mass-action kinetics) described by such planar autonomous ODEs, where $n$ is equal to the maximum order of the chemical reactions in the system. Analogues of the Hilbert number $H(n)$ for three different classes of chemical reaction systems are investigated: (i) chemical systems with reactions up to the $n$-th order; (ii) systems with up to $n$-molecular chemical reactions; and (iii) weakly reversible chemical reaction networks. In each case (i), (ii) and (iii), the question on the number of limit cycles is considered. Lower bounds on the modified Hilbert numbers are provided for both algebraic and non-algebraic limit cycles. Furthermore, given a general algebraic curve $h(x,y)=0$ of degree $n_h \in {\mathbb N}$ and containing one or more ovals in the positive quadrant, a chemical system is constructed which has the oval(s) as its stable algebraic limit cycle(s). The ODEs describing the dynamics of the constructed chemical system contain polynomials of degree at most $n=2\,n_h+1.$ Considering $n_h \ge 4,$ the algebraic curve $h(x,y)=0$ can contain multiple closed components with the maximum number of ovals given by Harnack's curve theorem as $1+(n_h-1)(n_h-2)/2$, which is equal to 4 for $n_h=4.$ Algebraic curve $h(x,y)=0$ with $n_h=4$ and the maximum number of four ovals is used to construct a chemical system which has four stable algebraic limit cycles.

math.DS

Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling

The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem.

q-bio.QM

Macroscopic description of a heavy particle immersed within a flow of light particles

A micro-hydrodynamics model based on elastic collisions of light point solvent particles with a heavy solute particle is investigated in the setting where the light particles have velocity distribution corresponding to a background flow. Considering a range of stationary background flows and distributions for the solvent particle velocities, the macroscopic Langevin-type description of the behaviour of the heavy particle is derived in the form of a generalized Ornstein-Uhlenbeck process. At leading order, the drift term in this process depends upon both the geometric structure of the background flow and the size of the heavy particle, while both drift and diffusion terms scale with moments of the light particle velocity distribution. Computational methods for simulating the micro-hydrodynamics model are then designed to confirm the theoretical results. To enable long-time stochastic simulations, simulations are performed in a frame co-moving with the heavy particle. Efficient methods for sampling the position and velocity distributions of incoming solvent particles at the boundaries of the co-moving frame are derived for a range of distributions of solvent particles. The simulations show good agreement with the theoretical results.

physics.flu-dyn

Asymmetric periodic boundary conditions for molecular dynamics and coarse-grained simulations of nucleic acids

Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is placed in the middle of a solvation box, which is chosen 'sufficiently large' to minimize any numerical artefacts associated with the periodic boundary conditions. This practical approach brings limitations to the size of biological systems that can be simulated. Here, we study simulations of effectively infinitely-long nucleic acids, which are solvated in the directions perpendicular to the polymer chain, while periodic boundary conditions are also applied along the polymer chain. We study the effects of these asymmetric periodic boundary conditions (APBC) on the simulated results, including the mechanical properties of biopolymers and the properties of the surrounding solvent. To get some further insights into the advantages of using the APBC, a coarse-grained worm-like chain model is first studied, illustrating how the persistence length can be extracted from local properties of the polymer chain, which are less affected by the APBC than some global averages. This is followed by all-atom molecular dynamics simulations of DNA in ionic solutions, where we use the APBC to investigate sequence-dependent properties of DNA molecules and properties of the surrounding solvent.

cond-mat.soft

Symmetries of many-body systems imply distance-dependent potentials

Considering interatomic potential $U({\mathbf q})$ where ${\mathbf q} = [{\mathbf q}_1, {\mathbf q}_2, \dots, {\mathbf q}_N] \in {\mathbb R}^{3N}$ is a vector describing positions, $\mathbf{q}_i \in {\mathbb R}^3$, it is shown that $U$ can be defined as a function of the interatomic distance variables $r_{ij} = |{\mathbf q}_i - {\mathbf q}_j |$, provided that the potential $U$ satisfies some symmetry assumptions. Moreover, the potential $U$ can be defined as a function of a proper subset of the distance variables $r_{ij}$, provided that $N > 5$, with the number of distance variables used scaling linearly with the number of atoms, $N$.

physics.class-ph

Chemical systems with limit cycles

The dynamics of a chemical reaction network (CRN) is often modelled under the assumption of mass action kinetics by a system of ordinary differential equations (ODEs) with polynomial right-hand sides that describe the time evolution of concentrations of chemical species involved. Given an arbitrarily large integer $K \in {\mathbb N}$, we show that there exists a CRN such that its ODE model has at least $K$ stable limit cycles. Such a CRN can be constructed with reactions of at most second order provided that the number of chemical species grows linearly with $K$. Bounds on the minimal number of chemical species and the minimal number of chemical reactions are presented for CRNs with $K$ stable limit cycles and at most second order or seventh order kinetics. We also show that CRNs with only two chemical species can have $K$ stable limit cycles, when the order of chemical reactions grows linearly with $K$.

math.DS

On Stretching, Bending, Shearing and Twisting of Actin Filaments I: Variational Models

Mechanochemical simulations of actomyosin networks are traditionally based on one-dimensional models of actin filaments having zero width. Here, and in the follow up paper, approaches are presented for more efficient modelling which incorporates stretching, bending, shearing and twisting of actin filaments. Our modelling of a semi-flexible filament with a small but finite width is based on the Cosserat theory of elastic rods, which allows for six degrees of freedom at every point on the filament's backbone. In the variational models presented in this paper, a small and discrete set of parameters is used to describe a smooth filament shape having all degrees of freedom allowed in the Cosserat theory. Two main approaches are introduced: one where polynomial spline functions describe the filament's configuration, and one in which geodesic curves in the space of the configurational degrees of freedom are used. We find that in the latter representation the strain energy function can be calculated without resorting to a small-angle expansion, so it can describe arbitrarily large filament deformations without systematic error. These approaches are validated by a dynamical model of a Cosserat filament, which can be further extended by using multi-resolution methods to allow more detailed monomer-based resolution in certain parts of the actin filament, as introduced in the follow up paper. The presented framework is illustrated by showing how torsional compliance in a finite-width filament can induce broken chiral symmetry in the structure of a cross-linked bundle.

cond-mat.soft

On Stretching, Bending, Shearing and Twisting of Actin Filaments II: Multi-Resolution Modelling

We present a multi-resolution methodology for modelling F-actin filaments. It provides detailed microscopic information at the level of individual monomers at a lower computational cost by replacing the monomer-based model in parts of the simulated filament by a rod-based macroscopic model. In the monomer-based description, G-actin is represented by ellipsoids bound at the surface in a double helical configuration to form F-actin. The rod-based model is coarser, in which F-actin is described using a Cosserat model, as seen in the preceding paper [arXiv:2112.01480]. The multi-resolution methodology is illustrated using three case studies, designed to test the properties of F-actin under stretching, bending, shearing and twisting. The methodology is especially suited for situations where filaments are subject to bending deformations. We investigate the limitations of using the standard Cosserat model to capture the complete torsional behaviour of F-actin, presenting its extensions which account for curvature dependent rigidities and a twist-stretch coupling to improve accuracy of the overall multi-resolution scheme.

cond-mat.soft

On standardised moments of force distribution in simple liquids

The force distribution of a tagged atom in a Lennard-Jones fluid in the canonical ensemble is studied with a focus on its dependence on inherent physical parameters: number density ($n$) and temperature ($T$). Utilising structural information from molecular dynamics simulations of the Lennard-Jones fluid, explicit analytical expressions for the dependence of standardised force moments on $n$ and $T$ are derived. Leading order behaviour of standardised moments of the force distribution are obtained in the limiting cases of small density ($n \rightarrow 0$) and low temperature ($T \rightarrow 0$), while the variations in the standardised moments are probed for general $n$ and $T$ using molecular dynamics simulations. Clustering effects are seen in molecular dynamics simulations and their effect on these standardised moments is discussed.

cond-mat.soft

On the counting function of semiprimes

A semiprime is a natural number which can be written as the product of two primes. The asymptotic behaviour of the function $π_2(x)$, the number of semiprimes less than or equal to $x$, is studied. Using a combinatorial argument, asymptotic series of $π_2(x)$ is determined, with all the terms explicitly given. An algorithm for the calculation of the constants involved in the asymptotic series is presented and the constants are computed to 20 significant digits. The errors of the partial sums of the asymptotic series are investigated. A generalization of this approach to products of $k$ primes, for $k\geq 3$, is also proposed.

math.NT

Identifiability of Stochastically Modelled Reaction Networks

Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous time Markov processes. In this manuscript, the identifiability of the underlying network structure with a given stochastic system dynamics is studied. It is shown that some data types related to the associated stochastic dynamics can uniquely identify the underlying network structure as well as the system parameters. The accuracy of the presented network inference is investigated when given dynamical data is obtained via stochastic simulations.

math.PR

Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions

Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or multi-resolution methodologies address this difficulty by using molecular dynamics (MD) and coarse-grained models in different parts of the cell. Their applicability depends on the accuracy and properties of the coarse-grained model which approximates the detailed MD description. A family of stochastic coarse-grained (SCG) models, written as relatively low-dimensional systems of nonlinear stochastic differential equations, is presented. The nonlinear SCG model incorporates the non-Gaussian force distribution which is observed in MD simulations and which cannot be described by linear models. It is shown that the nonlinearities can be chosen in such a way that they do not complicate parametrization of the SCG description by detailed MD simulations. The solution of the SCG model is found in terms of gamma functions.

physics.comp-ph

Limiting stochastic processes of shift-periodic dynamical systems

A shift-periodic map is a one-dimensional map from the real line to itself which is periodic up to a linear translation and allowed to have singularities. It is shown that iterative sequences $x_{n+1}=F(x_n)$ generated by such maps display rich dynamical behaviour. The integer parts $\lfloor x_n \rfloor$ give a discrete-time random walk for a suitable initial distribution of $x_0$ and converge in certain limits to Brownian motion or more general Lévy processes. Furthermore, for certain shift-periodic maps with small holes on $[0,1]$, convergence of trajectories to a continuous-time random walk is shown in a limit.

math.DS