A theory of the dynamics of DNA loop initiation in condensin/cohesin complexes

The structural maintenance of chromosome complexes exhibit the remarkable ability to actively extrude DNA, which has led to the appealing and popular "loop extrusion" model to explain one of the most important processes in biology: the compaction of chromatin during the cell cycle. A potential mechanism for the action of extrusion is the classic Brownian ratchet, which requires short DNA loops to overcome an initial enthalpic barrier to bending, before favoured entropic growth of longer loops. We present a simple model of the constrained dynamics of DNA loop formation based on a frictional worm like chain, where for circular loops of order, or smaller than the persistence length, internal friction to bending dominates solvent dynamics. Using Rayleigh's dissipation function, we show how bending friction can be translated to simple one dimensional diffusion of the angle of the loop resulting in a Smoluchowski equation with a coordinate dependent diffusion constant. This interplay between Brownian motion, bending dissipation and geometry of loops leads to a qualitatively new phenomenon, where the friction vanishes for bends with an angle of exactly 180°, due to a decoupling between changes in loop curvature and angle. Using this theory and given current parameter uncertainties, we tentatively predict mean first passage times of between 1 and 10 seconds, which is of order the cycle time of ATP, suggesting spontaneous looping could be sufficient to achieve efficient initiation of looping.

A Thermodynamically Consistent Model of Quasibrittle Elastic Damaged Materials Based on a Novel Helmholtz Potential and Dissipation Function

In the paper, a thermodynamically consistent model of elastic damaged material in the framework of small strain theory is formulated, describing the process of deterioration in quasibrittle materials, concrete in particular. The main goal is to appropriately depict the distinction between material responses in tension and compression. A novel Helmholtz energy and a dissipation potential including three damage parameters are introduced. The Helmholtz function has a continuous first derivative with respect to strain tensor. Based on the assumed functions, the strain–stress relationship, the damage condition, the evolution laws, and the tangent stiffness tensor are derived. The model’s predictions for uniaxial tension, uniaxial compression, uniaxial cyclic compression–tension, and pure shear tests are calculated using Wolfram Mathematica in order to identify the main features of the model and to grasp the physical meaning of an isotropic damage parameter, a tensile damage parameter, and a compressive damage parameter. Their values can be directly bound to changes of secant stiffness and generalized Poisson’s ratio. An interpretation of damage parameters in association with three mechanisms of damage is given. The considered dissipation potential allows a flexible choice of a damage condition. The influence of material parameters included in dissipation function on damage mode interaction is discussed.

Shear-Driven Mechanism of Temperature Gradient Formation in Microfluidic Nematic Devices: Theory and Numerical Studies

The purpose of this paper is to show some routes in describing the mechanism responsible for the formation of the temperature difference ΔT at the boundaries of the microfluidic hybrid aligned nematic (HAN) channel, initially equal to zero, if one sets up the stationary hydrodynamic flow vst or under the effect of an externally applied shear stress (SS) to the bounding surfaces. Calculations based on the nonlinear extension of the classical Ericksen–Leslie theory, supplemented by thermomechanical correction of the SS σzx and Rayleigh dissipation function while accounting for the entropy balance equation, show that the ΔT is proportional to the heat flux q across the HAN channel and grows by up to several degrees under the influence of the externally applied SS. The role of vst=ust(z)i^ with a sharp triangular profile ust(z) across the HAN in the production of the highest ΔT is also investigated.

Observability, controllability and stability analysis of discrete time engineering dynamic systems by means of Lagrangian, Hamiltonian and dissipative functions in discrete forms

Purpose The purpose of this paper is to analyze the dynamical state of a discrete time engineering/physical dynamic system. The analysis is performed based on observability, controllability and stability first using difference equations of generalized motion obtained through discrete time equations of dissipative generalized motion derived from discrete Lagrange-dissipative model [{L,D}-model] for short of a discrete time observed dynamic system. As a next step, the same system has also been analyzed related to observability, controllability and stability concepts but this time using discrete dissipative canonical equations derived from a discrete Hamiltonian system together with discrete generalized velocity proportional Rayleigh dissipation function. The methods have been applied to a coupled (electromechanical) example in different formulation types. Design/methodology/approach An observability, controllability and stability analysis of a discrete time observed dynamic system using discrete equations of generalized motion obtained through discrete {L,D}-model and discrete dissipative canonical equations obtained through discrete Hamiltonian together with discrete generalized velocity proportional Rayleigh dissipation function. Findings The related analysis can be carried out easily depending on the values of classical elements. Originality/value Discrete equations of generalized motion and discrete dissipative canonical equations obtained by discrete Lagrangian and discrete Hamiltonian, respectively, together with velocity proportional discrete dissipative function are used to analyze a discrete time observed engineering system by means of observability, controllability and stability using state variable theory and in the method proposed, the physical quantities do not need to be converted one to another.

A Dissipation Function–Based Method for Calculating the Energy Loss of Intracranial Aneurysms

At present, the energy loss (EL) mechanism of intracranial aneurysm (IA) rupture is explored based on the global EL calculated by Bernoulli equation, but the details of EL are still unclear. This study aimed to explore the temporal and spatial characteristics of EL of IAs and reveal its mechanism. A novel method for calculating the EL of IAs based on dissipation function (DF) was proposed. DF was derived from the differential form of the energy equation and reflected the irreversible conversion from mechanical energy to internal energy caused by the friction between the fluid micelles. Eight sidewall IAs located at the posterior communicating segment of the internal carotid artery were collected; the three-dimensional (3D) geometric models of IAs were established employing image segmentation and 3D reconstruction. Computational fluid dynamics was applied to obtain hemodynamic parameters of IAs. The temporal and spatial characteristics of EL of IAs were achieved utilizing our proposed method. The simulation results indicated that EL occurred mainly in the boundary layer and the region adjacent to high-velocity inflow jet, EL increased rapidly during cardiac systole and reached its maximum at end-systolic phase and then decreased gradually during diastole until the end of cardiac cycle. The proposed method achieved some improvements over the traditional Bernoulli equation–based method by acquiring the temporal and spatial characteristics of EL, and it could provide insights into the EL of IAs and contribute to further rupture mechanism investigation.

A rigorous derivation and energetics of a wave equation with fractional damping

We consider a linear system that consists of a linear wave equation on a horizontal hypersurface and a parabolic equation in the half space below. The model describes longitudinal elastic waves in organic monolayers at the water–air interface, which is an experimental setup that is relevant for understanding wave propagation in biological membranes. We study the scaling regime where the relevant horizontal length scale is much larger than the vertical length scale and provide a rigorous limit leading to a fractionally damped wave equation for the membrane. We provide the associated existence results via linear semigroup theory and show convergence of the solutions in the scaling limit. Moreover, based on the energy–dissipation structure for the full model, we derive a natural energy and a natural dissipation function for the fractionally damped wave equation with a time derivative of order 3/2.

Heat Driven Flows in Microsized Nematic Volumes: Computational Studies and Analysis

The nematic fluid pumping mechanism responsible for the heat driven flow in microfluidic nematic channels and capillaries is described in a number of applications. This heat driven flow can be generated either by a laser beam focused inside the nematic microvolume and at the nematic channel boundary, or by inhomogeneous heating of the nematic channel or capillary boundaries. As an example, the scenario of the vortex flow excitation in microsized nematic volume, under the influence of a temperature gradient caused by the heat flux through the bounding surface of the channel, is described. In order to clarify the role of heat flux in the formation of the vortex flow in microsized nematic volume, a number of hydrodynamic regimes based on a nonlinear extension of the Ericksen–Leslie theory, supplemented by thermomechanical correction of the shear stress and Rayleigh dissipation function, as well as taking into account the entropy balance equation, are analyzed. It is shown that the features of the vortex flow are affected not only by the power of the laser radiation, but also by the duration of the energy injection into the microsized nematic channel.

Energy of a free Brownian particle coupled to thermal vacuum

Experimentalists have come to temperatures very close to absolute zero at which physics that was once ordinary becomes extraordinary. In such a regime quantum effects and fluctuations start to play a dominant role. In this context we study the simplest open quantum system, namely, a free quantum Brownian particle coupled to thermal vacuum, i.e. thermostat in the limiting case of absolute zero temperature. We analyze the average energy $$E=E(c)$$ E = E ( c ) of the particle from a weak to strong interaction strength c between the particle and thermal vacuum. The impact of various dissipation mechanisms is considered. In the weak coupling regime the energy tends to zero as $$E(c) \sim c\, \ln {(1/c)}$$ E ( c ) ∼ c ln ( 1 / c ) while in the strong coupling regime it diverges to infinity as $$E(c) \sim \sqrt{c}$$ E ( c ) ∼ c . We demonstrate it for selected examples of the dissipation mechanisms defined by the memory kernel $$\gamma (t)$$ γ ( t ) of the Generalized Langevin Equation. We reveal how at a fixed value of c the energy E(c) depends on the dissipation model: one has to compare values of the derivative $$\gamma '(t)$$ γ ′ ( t ) of the dissipation function $$\gamma (t)$$ γ ( t ) at time $$t=0$$ t = 0 or at the memory time $$t=\tau _c$$ t = τ c which characterizes the degree of non-Markovianity of the Brownian particle dynamics. The impact of low temperature is also presented.

ODREĐIVANJE TERMIČKIH VELIČINA KOD PRAVOLINIJSKOG KLIZNOG LEŽIŠTA NA BAZI DISIPACIONE FUNKCIJE

In the first part of the paper, the continuity equation in the boundary layer for stationary two-dimensional flow is derived on the basis of the law of mass conservation. After that, using Newton's second law for control volume, the equation for the momentum was derived. Using the derived equations, the analysis was performed with respect to the influence of temperature. After that, on the basis of the energy balance, an energy equation was derived in which a viscous dissipation function was introduced, which enabled a wider application. At the end of the paper, the derived equations were applied to a specific calculation example from technical practice in the calculation of thermal quantities in a rectilinear sliding bearing, which was the aim of the work

Violations of the Clausius–Duhem inequality in Couette flows of granular media

Spontaneous violations of the Clausius–Duhem (CD) inequality in Couette-type collisional flows of model granular media are studied. Planar systems of monosized circular discs (with disc numbers from 10 to 204, and disc diameters from 0.001 m to 1 m) with frictional-Hookean contacts are simulated under periodic boundary conditions by a molecular dynamics. The scale-dependent homogenization of micropolar media is used to determine the energy balances and mechanical entropy production. The dissipation function exhibits spontaneous negative entropy increments described by the fluctuation theorem. The boundary between violations and non-violations of the CD inequality is mapped in the parameter space, where the probability of such events diminishes with the disc diameter, the disc number and the area fraction increasing. The dissipation function is a random process, tending to Gaussian as the number of discs increases, and possessing non-trivial fractal and anti-persistent Hurst properties.