arXiv subjects

Patrick BarAvi

Publications and source records attributed to Patrick BarAvi.

5 recordsLinked to original sources

arXiv2026

Deformable Charge Dynamics in Biological Environments: An Extended Structural Dynamics Foundation for Biological Electrostatics

The point-charge approximation is one of the most successful idealizations in molecular biophysics, but it becomes strained in strong fields, confined geometries, and crowded aqueous environments. We develop a minimal Extended Structural Dynamics (ESD) model in which charged entities are treated as finite, deformable objects with an internal breathing mode rather than as structureless points. Starting from a Hamiltonian description and a controlled coarse-graining procedure, we derive an effective generalized Langevin equation for the center-of-mass motion. The reduced dynamics contain a memory kernel with three physically distinct contributions: finite-size causal delay, inertial deformation, and crowding-induced deformation. The derivation rests on explicit assumptions of small deformation, local dielectric screening, one dominant internal mode, and adiabatic elimination of the fast structural coordinate. Parameters are determined by independently measurable inputs -- ionic radius, charge, mass, and the high-frequency dielectric constant of water -- with one exception: the dimensionless coupling lambda governing crowding-induced deformation, discussed in detail in the paper. Two primary predictions follow. First, transport through confined geometries should show dynamical deviations from point-charge baselines scaling with ionic deformability, beyond static potential-of-mean-force predictions. Second, polarization response should preserve ionic-radius ordering across alkali ions. Two secondary consequences are identified: a field-dependent effective charge radius and a deformation-dependent correction to near-surface mobility. Amplification of these effects in confined settings is treated as a plausible extension rather than a derived result. The framework recovers standard electrostatic models as limiting cases.

cond-mat.soft↗

arXiv2026

Anomalous Diffusion as Structural Memory: An Extended Structural Dynamics Approach

Sub-diffusion in biological systems is conventionally treated as anomalous, requiring fractional derivatives, heavy-tailed waiting times, or fitted memory kernels. We argue that this anomaly is an artifact of an incomplete phase space. Standard frameworks model diffusing particles as points. Biological molecules are not points. They are three-dimensional deformable entities whose position, orientation, and internal structure are irreducible physical properties, not modeling conveniences appended to a point mass. Within the Extended Structural Dynamics (ESD) framework, each particle is a primitive structured entity with translational, orientational, and deformational degrees of freedom. When dynamics on this full phase space are projected onto the translational subspace alone, a memory kernel emerges from the projection without phenomenological postulate. The subdiffusion exponent is determined by the internal mode spectrum, independently measurable from B-factors, NMR order parameters, or molecular dynamics simulations, without fitting to transport data. Four falsifiable predictions follow: subdiffusion strength correlates with molecular flexibility; temperature drives crossover to normal diffusion at a characteristic energy scale set by internal mode frequencies; a non-zero rotation-translation cross-correlation spectrum encodes internal dynamics, identically zero in point-particle models; and memory timescales scale as the square of particle size. Quantitative consistency with experimental observations for proteins in crowded media is demonstrated using independently estimated structural parameters. What appears anomalous from the point-particle perspective is the expected behavior of structured matter projected onto an impoverished description. The anomaly is not in the physics. It is in the phase space.

cond-mat.stat-mech↗

arXiv2026

Extended Structural Dynamics and the Lorentz Abraham Dirac Equation: A Deformable Charge Interpretation

Radiation reaction in classical electrodynamics is traditionally described by the Lorentz Abraham Dirac equation (LAD), whose point particle formulation leads to well known difficulties including runaway solutions, pre acceleration, and the ambiguous status of the Schott term. We analyze radiation reaction within the framework of Extended Structural Dynamics (ESD), in which charged particles are modeled as finite systems possessing internal dynamical structure. In the present formulation the particle is represented as a finite, deformable sphere with a single radial breathing mode describing internal charge redistribution. This internal degree of freedom introduces a finite response time and ensures that changes in the charge distribution propagate at finite speed. Starting from the full particle field Hamiltonian, we derive the retarded self force for such a deformable charge and obtain a delay kernel that depends on both the past motion and the past internal configuration. In the adiabatic regime the kernel reduces to an effective causal form that is free of pre acceleration and exhibits a band pass frequency response, suppressing high frequency instabilities associated with runaway behavior. The Schott term is shown to correspond to reversible energy stored in the internal deformation mode, providing a direct mechanical interpretation of this contribution. The LAD dynamics are recovered only in the double limit of vanishing spatial extent and frozen internal dynamics, where the causal delay structure collapses to the familiar point particle approximation. Within this framework radiation reaction arises as the leading order effective dynamics of a finite deformable charge, while higher order corrections encode finite size and internal structural effects without modifying Maxwell's equations or introducing ad hoc regularization.

physics.class-ph↗

arXiv2026

Structural Viscosity, Thermal Waves, and the Mpemba Effect from Extended Structural Dynamics

Classical hydrodynamics rests on the point-particle idealization, leading to parabolic transport equations, infinite signal speeds, and the inability to capture finite time relaxation, anisotropic transport, or non Fourier thermal phenomena. This work introduces Extended Structural Dynamics (ESD), a kinetic framework in which constituents are described as spatially extended objects possessing orientation, angular momentum, and internal deformation modes. Starting from an extended Boltzmann equation, a Chapman Enskog expansion with BGK closure yields two hyperbolic parabolic transport laws: a dynamical spin equation coupling orientational relaxation to fluid vorticity, and a heat flux relaxation equation with structural thermal conductivity. These equations predict finite propagation speeds for momentum and heat, intrinsic shock regularization, anisotropic transport, and thermal waves. The spin equation provides a kinetic derivation of micropolar fluid theory, while the heat flux equation supplies a microscopic foundation for Cattaneo Vernotte behavior. Quantitative estimates indicate structural contributions can dominate classical transport coefficients. The BGK closure preserves the qualitative geometric structure of extended phase space and captures correct scaling; the connection between the orientational relaxation time and Lyapunov instability is established independently. The resulting scaling laws follow from rotational-translational coupling. Predictions include Mpemba crossover time for colloidal ellipsoids and shock width for asymmetric molecules, both testable with existing techniques.

cond-mat.stat-mech↗

arXiv2025

Geometric Irreversibility - Enriching Lanford's Theorem with Orientational and Deformable Degrees of Freedom

We propose an extended structural dynamics framework that enriches classical mechanics by treating particle orientation and internal structure as fundamental phase-space coordinates. This extension preserves Hamiltonian structure and Liouville invariance while revealing two distinct mechanisms for entropy production: (i) collisional randomization through orientation-dependent scattering (generalizing Boltzmann), and (ii) continuous geometric instability arising from rotational-deformational coupling. We argue this dual-mechanism structure provides a dynamical justification for the molecular chaos assumption central to Boltzmann-Lanford derivations, particularly in regimes (dense systems, few bodies, structured particles) where classical point-particle theory fails. Recent mathematical advances (Deng, Hani & Ma 2024) extend Lanford's theorem to arbitrary times but still require molecular chaos as input and apply only to dilute gases. This extended structural framework addresses the complementary philosophical question: how can molecular chaos itself emerge from deterministic dynamics? We show that geometric instability in extended phase space makes entropy-decreasing trajectories dynamically unstable, offering a structural explanation for the Second Law. This reframes thermodynamic irreversibility as a geometric property of structured motion rather than a purely statistical postulate.

cond-mat.stat-mech↗