arXiv subjects

Mesfin Asfaw Taye

Publications and source records attributed to Mesfin Asfaw Taye.

15 recordsLinked to original sources

arXiv2026

A microscopic heat engine with many hidden variables

Microscopic motors are commonly monitored through a single mechanical coordinate, whereas the chemical, conformational, or rotational cycles that sustain their motion remain unresolved. Mechanical stall is defined by the vanishing of the mean observed velocity; this scalar condition, however, does not generally imply thermodynamic reversibility. We analyze an overdamped Brownian motor in which one observed coordinate is coupled to several internal phases through a single shared interaction potential. Because the transmitted force and the reaction torques derive from the same energy, the resulting rank-one reciprocal structure yields an exact pointwise identity between the observed and hidden probability currents. This identity provides an exact expression for the entropy production at stall for an arbitrary periodic interaction. In particular, a positive current-square dissipation in the mechanical channel, defined from the full stationary state through the coupling-coordinate-resolved local velocity, determines together with the stall load the collective hidden current projected onto the coupling direction. The stationary one-coordinate marginal current nevertheless vanishes identically at stall; consequently, the stationary marginal density and mean displacement current do not determine this dissipation. Hidden currents orthogonal to the coupling direction dissipate without affecting the observed motion and generate an irreducible contribution that cannot be inferred from the rank-one mechanical channel.

cond-mat.stat-mech↗

arXiv2026

Stochastic First-Passage Theory of HIV Viral Rebound Following Latent Reservoir Reactivation

In our earlier work, we modeled the stochastic initiation of HIV rebound by treating latent-cell reactivation as a Poisson-driven process during antiretroviral-therapy (ART) washout, immune modulation, and therapeutic perturbation~\cite{Taye2025CM}. That framework characterized activation survival, cumulative hazards, waiting-time laws, and expected viral-load trajectories. However, the endpoint observed in analytical treatment interruption (ATI) studies is not the hidden time of first successful reactivation. It is the first time at which plasma virus exceeds an assay-defined detection threshold. Here we reformulate post-treatment rebound as a stochastic first-passage problem, with $T_{\rm reb}=\inf\{t\ge t_w:V(t)\ge V_{\rm det}\}$. Successful reactivation events arrive with a time-dependent intensity, and each event seeds an exponentially expanding viral lineage. The total plasma viral load is therefore a Poisson shot-noise process, and rebound corresponds to its first threshold crossing. In the rare-reactivation regime, this crossing is dominated by the earliest successful lineage. Rebound timing then separates into two components: a stochastic waiting time for reservoir reactivation and a deterministic growth delay to detectability. This separation gives a shifted-hazard survival law and yields closed-form rebound-time distributions for constant activation, ART-washout-dependent activation, immune-periodic activation, Cox-process activation, and heterogeneous-reservoir activation. The same formulation also provides a likelihood suitable for the interval-censored sampling structure of ATI trials.

physics.bio-ph↗

arXiv2026

Biological Time, Evolutionary Optimization, and Gauge Coherence: A Thermodynamic Synthesis of the Principle of Biological Time Equivalence

Biological theory usually treats time as an external chronological variable against which growth, aging, and ecological change are parametrized. Yet living systems also generate an internal measure of duration through physiological cycling and irreversible entropy production, and the regularities of allometric lifespan scaling, biological clocks, life-history evolution, ecological synchronization, and disease are ordinarily studied in isolation rather than within a single thermodynamic internal-time framework. The Principle of Biological Time Equivalence (PBTE) proposes such a framework.

physics.bio-ph↗

arXiv2026

Relativistic PBTE:Biological Proper Time Along the Worldline

Biological aging is conventionally indexed by chronological time, yet every organism is a physical system tracing a worldline through spacetime, so the time available to its metabolism is not coordinate time $t$ but relativistic proper time $τ$. Building on the established Principle of Biological Time Equivalence (PBTE), whose thermodynamic foundation and aging dynamics are taken here as prior results \citep{TayeBook2026,TayeAging2026,TayeCardiac2026}, we ask how internal physiological time relates to the proper time of physics. The central result is that biological age is an entropy-production functional evaluated along the proper-time worldline, \begin{equation*} A_{\rm PBTE}=\frac{1}{Σ_{\rm ref}}\int_{τ_0}^{τ_1}\dotΣ_p(τ)\,dτ, \qquad \frac{dA_{\rm PBTE}}{dt}=\frac{\dotΣ_p}{γ\,Σ_{\rm ref}}, \end{equation*} where $\dotΣ_p$ is entropy production per unit proper time in the local rest frame and $γ$ the Lorentz factor.

physics.bio-ph↗

arXiv2025

Curzon Ahlborn Type Efficiency in a Brownian Heat Engine with Exponential Temperature Profile

We investigate a Brownian heat engine wherein a particle moves through a periodic ratchet potential under an exponentially decreasing temperature profile, a spatial configuration that closely resembles experimentally realizable conditions such as laser-induced thermal gradients and thermoplasmonic heating. This model yields exact analytical expressions for the particle current, thermodynamic efficiency, entropy production, and coefficient of performance (COP), and uniquely recovers the Curzon Ahlborn efficiency and the corresponding endoreversible COP exactly in the quasistatic limit. These findings provide a rare and rigorous realization of endoreversible thermodynamics at the mesoscopic scale because they are derived directly from microscopic stochastic dynamics without recourse to phenomenological assumptions, asymptotic approximations or coarse-graining techniques. Although the derived efficiency and COP are exact, they remain strictly below the Carnot limit, reflecting the inherent irreversibility embedded within the endoreversible framework. Furthermore, we show that in comparison to linear and piecewise-constant temperature profile cases, the exponential temperature profile leads to significantly higher particle velocities, higher entropy production, but lower thermodynamic efficiency, which underscores the fundamental trade-off between transport speed and energy cost.

cond-mat.stat-mech↗

arXiv2022

The efficacy of antiviral drug, HIV viral load and the immune response

Developing antiviral drugs is an exigent task since viruses mutate to overcome the effect of antiviral drugs. As a result, the efficacy of most antiviral drugs is short-lived. To include this effect, we modify the Neumann and Dahari model. Considering the fact that the efficacy of the antiviral drug varies in time, the differential equations introduced in the previous model systems are rewritten to study the correlation between the viral load and antiviral drug. The effect of antiviral drug that either prevents infection or stops the production of a virus is explored. First, the efficacy of the drug is considered to decreases monotonously as time progresses. In this case, our result depicts that when the efficacy of the drug is low, the viral load decreases and increases back in time revealing the effect of the antiviral drugs is short-lived. On the other hand, for the antiviral drug with high efficacy, the viral load, as well as the number of infected cells, monotonously decreases while the number of uninfected cells increases. The dependence of the critical drug efficacy on time is also explored. Moreover, the correlation between viral load, the antiviral drug, and CTL response is also explored. In this case, not only the dependence for the basic reproduction ratio on the model parameters is explored but also we analyze the critical drug efficacy as a function of time. We show that the term related to the basic reproduction ratio increases when the CTL response step up. A simple analytically solvable mathematical model is also presented to analyze the correlation between viral load and antiviral drugs.

physics.bio-ph↗

arXiv2021

Effect of viscous friction on entropy, entropy production and entropy extraction rates in underdamped and overdamped media

Considering viscous friction that varies spatially and temporally, the general expressions for entropy production, free energy, and entropy extraction rates are derived to a Brownian particle that walks in an overdamped and underdamped media. Via the well known stochastic approaches to underdamped and overdamped media, the thermodynamic expressions first derived at trajectory level then generalized to an ensemble level. To study the non-equilibrium thermodynamic features of a Brownian particle that hops in a medium where its viscosity varies on time, a Brownian particle that walks on a periodic isothermal medium (in the presence or absence of load) is considered. The exact analytical results depict that in the absence of load $f=0$, the entropy production rate ${\dot e}_{p}$ approaches the entropy extraction rate ${\dot h}_{d}=0$. This is reasonable since any system which is in contact with a uniform temperature should obey the detail balance condition in a long time limit. In the presence of load and when the viscous friction decreases either spatially or temporally, the entropy $S(t)$ monotonously increases with time and saturates to a constant value as $t$ further steps up. The entropy production rate ${\dot e}_{p}$ decreases in time and at steady state (in the presence of load), ${\dot e}_{p}={\dot h}_{d}>0$. On the contrary, when the viscous friction increases either spatially or temporally, the rate of entropy production as well as the rate of entropy extraction monotonously steps up showing that such systems are inherently irreversible.

cond-mat.stat-mech↗

arXiv2021

Entropy production and entropy extraction rates for a Brownian particle that walks in underdamped medium

The expressions for entropy production, free energy, and entropy extraction rates are derived for a Brownian particle that walks in an underdamped medium. Our analysis indicates that as long as the system is driven out of equilibrium, it constantly produces entropy at the same time it extracts entropy out of the system. At steady state, the rate of entropy production ${\dot e}_{p}$ balances the rate of entropy extraction ${\dot h}_{d}$. At equilibrium both entropy production and extraction rates become zero. The entropy production and entropy extraction rates are also sensitive to time. As time progresses, both entropy production and extraction rates increase in time and saturate to constant values. Moreover employing microscopic stochastic approach, several thermodynamic relations for different model systems are explored analytically and via numerical simulations by considering a Brownian particle that moves in overdamped medium. Our analysis indicates that the results obtained for underdamped cases quantitatively agree with overdamped cases at steady state. The fluctuation theorem is also discussed in detailed.

cond-mat.stat-mech↗

arXiv2019

The physics of Erythrocyte Sedimentation Rate

An erythrocytes sedimentation rate (ESR) measures how fast a blood sample sediments along a test tube in one hour in a clinical laboratory. Since elevated level of ESR is associated with inflammatory diseases, ESR is one of the routine hematology test in a clinical laboratory. In this paper, the physics of erythrocyte (RBC) sedimentation rate as well as the dynamics of the RBC is explored by modeling the dynamics of the cells as the motion of Brownian particle moving in a viscous medium. The viscous friction of blood $γ$ is considered to decrease as the temperature of the medium increases \cite{aa1}. The results obtained in this work show that the ESR increases as the number of red blood cells (that bind together in the sedimentation process) steps up. The room temperature also affects the sedimentation rate. As the room temperature rises up, the ESR steps up. Furthermore the dynamics of the RBC along a Westergren pipet that is held in an upright position is explored. The exact analytic result depicts that the velocity of cells increases as the number of cells that form rouleaux steps up. Since our study is performed by considering real physical parameters, the results obtained in this work non only agree with the experimental observations but also helps to understand most hematological experiments that are conducted in vitro.

physics.bio-ph↗

arXiv2016

First passage time and stochastic resonance of excitable systems

We study noise induced thermally activated barrier crossing of a Brownian particle that hops in a periodic ratchet potential where the ratchet potential is coupled with a spatially uniform temperature. The viscous friction is considered to decrease exponentially when the temperature $T$ of the medium increases as proposed originally by Reynolds. The results obtained in this work show that the mean first passage time of the particle is considerably lower when the viscous friction is temperature dependent than that of the case where the viscous friction is temperature independent. We then explore the thermally activated barrier crossing rate of the system in the presence of time varying signal. In this case, the interplay between noise and sinusoidal driving force in the bistable system may lead the system into stochastic resonance provided that the random tracks are adjusted in an optimal way to the recurring external force.

cond-mat.stat-mech↗

arXiv2016

Irreversible Brownian heat engine

We model a Brownian heat engine as a Brownian particle that hops in a periodic ratchet potential where the ratchet potential is coupled with a linearly decreasing background temperature. It is shown that the efficiency of such Brownian heat engine is far from Carnot efficiency even at quaistatic limit. At quasistatic limit, the efficiency of the heat engine approaches the efficiency of endoreversible engine $η=1-\sqrt{{T_{c}/T_{h}}}$ \cite{c18}. On the other hand, the maximum power efficiency of the engine approaches $η^{MAX}=1-({T_{c}/T_{h}})^{1\over 4}$. Moreover, the dependence of the current as well as the efficiency on the model parameters is explored analytically by omitting the heat exchange via the kinetic energy. In this case we show that the optimized efficiency always lies between the efficiently at quaistatic limit and the efficiency at maximum power. On the other hand, the efficiency at maximum power is always less than the optimized efficiency since the fast motion of the particle comes at the expense of the energy cost. The role of time on the performance of the motor is also explored via numerical simulations. Our numerical results depict that the time $t$ as well as the external load dictate the direction of the particle velocity. Moreover the performance of the heat engine improves with time. At large $t$ (steady state),the velocity, the efficiency and the coefficient of performance of the refrigerator attain their maximum value.

cond-mat.stat-mech↗

arXiv2016

Free energy and entropy production rate for a Brownian particle that walks on overdamped medium

We derive general expressions for the free energy, entropy production and entropy extraction rates for a Brownian particle that walks in a viscous medium where the dynamics of its motion is governed by the Langevin equation. It is shown that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In long time limit, the rate of entropy production balances the rate of entropy extraction and at equilibrium both entropy production and extraction rates become zero. Moreover, considering different model systems, not only we investigate how various thermodynamic quantities behave in time but also we discuss the fluctuation theorem in detail.

cond-mat.stat-mech↗

arXiv2015

Rectified motion of short polymer chain that walks along a ratchet potential that coupled with spatially varying temperature

We explore the transport features of a single flexible polymer chain that walks on a periodic ratchet potential coupled with spatially varying temperature. At steady state the polymer exhibits a fast unidirectional motion where the intensity of its current rectification depends strongly on its elastic strength and size. Analytic and numerical analysis reveal that the steady state transport of the polymer can be controlled by attenuating the strength of the elastic constant. Furthermore, the stall force at which the chain current vanishes is independent of the chain length and coupling strength. Far from the stall force the mobility of the chain is strongly dependent on its size and flexibility. These findings show how the mobility of a polymer can be controlled by tuning system parameters, and may have novel applications for polymer transport and sorting of multicomponent systems based on their dominant parameters.

cond-mat.soft↗

arXiv2015

The effect of temperature on viscous friction and the performance of a Brownian heat engine

We explore the transport features of a Brownian particle that walks in a periodic ratchet potential that is coupled with a spatially varying temperature background. Since the viscous friction of the medium decreases as the temperature of the medium increases, any reasonable exploration regarding the thermodynamic features of the Brownian engine should take into account the role of temperature on the viscosity of the fluid. In this work, we study this effect of temperature by considering a viscous friction that decreases exponentially as the background temperature increases. Our result depicts that the Brownian particle exhibits a fast unidirectional motion when the viscous friction is temperature dependent than that of constant viscous friction. Moreover the efficiency of this motor is considerably enhanced when the viscous friction is temperature dependent. On the hand, the motor exhibits a higher performance of the refrigerator when the viscose friction is taken to be constant.

cond-mat.stat-mech↗

arXiv2015

Exact analytical expressions for entropy production and free energy

The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time $t$. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extract entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to constant value. In long time limit, the rate of entropy production balances the rate of entropy extraction and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, not only many thermodynamic theories can be checked but also the wrong conclusions that are given due to lack of exact analytic expressions will be corrected.

cond-mat.stat-mech↗