Eckart Frame Research Articles

Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism.

Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule.

Scalar fluid in scalar-tensor gravity from an equivalent picture of thermodynamic and fluid descriptions of gravitational dynamics

We revisit the thermodynamic description of fluid, represented by scalar field in scalar-tensor gravity theory through a general approach to study the thermodynamics of relativistic fluids. In order to identify the fluid energy-momentum tensor, contrary to the existing way, we use equivalent description of gravitational dynamics both in Jordan and Einstein frames as thermodynamical identity and fluid equation on a generic null surface. Such an approach provides the energy-momentum tensors for scalar fluid as that of an ideal fluid in both the frames. We then mention few issues in the existing way of using Eckart's formalism for an ideal fluid. Our investigation suggests that the Eckart's frame may not be suitable to consider ideal fluid. Consequently a possible alternative description, valid in other than Eckart's frame, is being suggested for a general ideal fluid. Based on this we obtain a unified thermodynamic description in both Jordan and Einstein frames from our identified energy-momentum tensors. Finally, the relations between thermodynamic entities on different frames are being put forwarded. Thus, the description in either of the frames is enough to provide the complete picture.

Temperature in relativistic fluids

For static matter in a gravitational field, different conventions for equilibrium local temperature exist in the classic physics literature. We illustrate the difference between two popular conventions using black-body radiation in a spherically symmetric gravitational potential. Equilibrium temperatures defined by the "Landau frame" or "Eckart frame" prescriptions most commonly used in relativistic fluid dynamics do not satisfy the statistical-mechanical relation $1/T=dS/dE$.

Phenomenological Relativistic Second-Order Hydrodynamics for Multiflavor Fluids

In this work, we perform a phenomenological derivation of the first- and second-order relativistic hydrodynamics of dissipative fluids. To set the stage, we start with a review of the ideal relativistic hydrodynamics from energy–momentum and particle number conservation equations. We then go on to discuss the matching conditions to local thermodynamical equilibrium, symmetries of the energy–momentum tensor, decomposition of dissipative processes according to their Lorentz structure, and, finally, the definition of the fluid velocity in the Landau and Eckart frames. With this preparatory work, we first formulate the first-order (Navier–Stokes) relativistic hydrodynamics from the entropy flow equation, keeping only the first-order gradients of thermodynamical forces. A generalized form of diffusion terms is found with a matrix of diffusion coefficients describing the relative diffusion between various flavors. The procedure of finding the dissipative terms is then extended to the second order to obtain the most general form of dissipative function for multiflavor systems up to the second order in dissipative fluxes. The dissipative function now includes in addition to the usual second-order transport coefficients of Israel–Stewart theory also second-order diffusion between different flavors. The relaxation-type equations of second-order hydrodynamics are found from the requirement of positivity of the dissipation function, which features the finite relaxation times of various dissipative processes that guarantee the causality and stability of the fluid dynamics. These equations contain a complete set of nonlinear terms in the thermodynamic gradients and dissipative fluxes arising from the entropy current, which are not present in the conventional Israel–Stewart theory.

Symmetric-hyperbolic quasihydrodynamics

We set up a general framework for systematically building and classifying, in the linear regime, causal and stable dissipative hydrodynamic theories that, alongside with the usual hydrodynamic modes, also allow for an arbitrary number of nonhydrodynamic modes with complex dispersion relation (such theories are often referred to as ``quasihydrodynamic''). To increase the number of nonhydrodynamic modes, one needs to add more effective fields to the model. The system of equations governing this class of quasihydrodynamic theories is symmetric hyperbolic, thermodynamically consistent (i.e., the entropy is a Lyapunov function) and can be derived from an action principle. As a first application of the formalism, we prove that, in the linear regime, the Israel-Stewart theory in the Eckart frame and the Israel-Stewart theory in the Landau frame are exactly the same theory. In addition, with an Onsager-Casimir analysis, we show that in strongly coupled plasmas the nonequilibrium degrees of freedom typically appear in pairs, whose members acquire opposite phase under time reversal. We use this insight to modify Cattaneo's model for diffusion, in a way to make its initial transient consistent with the transient dynamics of holographic plasmas.

Molecular frames for a symmetry-adapted rotational basis set

In molecular ro-vibrational calculations, it is desirable to build a symmetry-adapted basis set where both the rotational and vibrational functions are each separately symmetrised. Enabling rotational symmetrisation requires the use of body-fixed frames whose rotations under molecular symmetry operations are constant. The familiar Eckart and Sayvetz frames are examples of such frames, as are bisector frames for certain molecules. In this work, we introduce alternative frames for CH3Cl-type molecules and C2H6 that can be used for rotational symmetrisation. These are defined by the vibrational coordinates without the need for a reference geometry. We also provide one method to find such frames. Finally, we state a straightforward transformation of the s-vectors when changing frames which facilitates the evaluation of kinetic energy operators in these non-standard frames.

On the derivation of the Landau–Lifshitz frame in relativistic kinetic theory

The Landau–Lifshitz frame has been widely used to represent the macroscopic quantities of relativistic hydrodynamics in the presence of the dissipative process. In this paper, we derive the Landau–Lifshitz frame in the near-equilibrium regime under self-contained assumptions that do not require comparison with the Eckart frame. And then we revisit the relativistic BGK model proposed by Anderson and Witting to provide an application example of the Landau–Lifshitz frame.

Relativistic extended thermodynamics of polyatomic gases in the Landau and Lifshitz description

In this article we generalize to polyatomic gases the moment closure of the relativistic Anderson–Witting model proposed by Cercignani and Kremer in the monatomic case, that uses the four-velocity in the Landau–Lifshitz description. A moment model is derived and compared with that recently proposed by Pennisi and Ruggeri using a variant of the Anderson–Witting model in an Eckart frame, obtaining that the balance equations and the collision term are equivalent up to first order with respect to equilibrium.

Cosmic Evolution of Viscous QCD Epoch in Causal Eckart Frame

It is conjectured that in cosmological applications the particle current is not modified but finite heat or energy flow. Therefore, comoving Eckart frame is a suitable choice, as it merely ceases the charge and particle diffusion and conserves charges and particles. The cosmic evolution of viscous hadron and parton epochs in casual and non-casual Eckart frame is analyzed. By proposing equations of state deduced from recent lattice QCD simulations including pressure p, energy density ρ, and temperature T, the Friedmann equations are solved. We introduce expressions for the temporal evolution of the Hubble parameter H˙, the cosmic energy density ρ˙, and the share η˙ and the bulk viscous coefficient ζ˙. We also suggest how the bulk viscous pressure Π could be related to H. We conclude that the relativistic theory of fluids, the Eckart frame, and the finite viscous coefficients play essential roles in the cosmic evolution, especially in the hadron and parton epochs.

Stationary models of magnetized viscous tori around a Schwarzschild black hole

We present stationary solutions of magnetized, viscous thick accretion disks around a Schwarzschild black hole. We assume that the tori are not self-gravitating, are endowed with a toroidal magnetic field, and obey a constant angular momentum law. Our study focuses on the role of the black hole curvature in the shear viscosity tensor and in their potential combined effect on the stationary solutions. Those are built in the framework of a causality-preserving, second-order gradient expansion scheme of relativistic hydrodynamics in the Eckart frame description which gives rise to hyperbolic equations of motion. The stationary models are constructed by numerically solving the general relativistic momentum conservation equation using the method of characteristics. We place constraints in the range of validity of the second-order transport coefficients of the theory. Our results reveal that the effects of the shear viscosity and curvature are particularly noticeable only close to the cusp of the disks. The surfaces of constant pressure are affected by viscosity and curvature and the self-intersecting isocontour - the cusp - moves to smaller radii (i.e. towards the black hole horizon) as the effects become more significant. For highly magnetized disks the shift in the cusp location is smaller. Our findings might have implications on the dynamical stability of constant angular momentum tori which, in the inviscid case, are affected by the runaway instability.

First order non-Lorentzian fluids, entropy production, and linear instabilities

In this note, we investigate linear instabilities of hydrodynamics with corrections up to first order in derivatives. It has long been known that relativistic (Lorentzian) first order hydrodynamics, with positive local entropy production, exhibits unphysical instabilities. We extend this analysis to fluids with Galilean and Carrollian boost symmetries. We find that the instabilities occur in all cases, except for fluids with Galilean boost symmetry combined with the choice of macroscopic variables called Eckart frame. We also present a complete linearised analysis of the full spectrum of first order Carrollian hydrodynamics. Furthermore, we show that even in a fluid without boost symmetry present, instabilities can occur. These results provide evidence that the unphysical instabilities are symptoms of first order hydrodynamics, rather than a special feature of Lorentzian fluids.

Third order viscous hydrodynamics from the entropy four current

Non-equilibrium dynamics for relativistic fluid or quark gluon plasma (QGP) have already been calculated earlier upto third order using both kinetic and thermodynamic approaches. Calculations presented in this manuscript are based on thermodynamics principles. The expressions for third order dissipative fluxes have been derived from equation for entropy 4-current developed earlier by A. Muronga. The relaxation equations in the present work have been developed in a simple Bjorken (1+1)D scenario and Eckart frame. The relaxation equations are found to have slightly different values for the coupling coefficients as compared to calculations from earlier models. The solutions to the differential equations have been found to be sensitive to values of these coefficients. The shear relaxation equations derived in third order theory are discussed term by term. Effects of third order theory on shear relaxation time has been discussed. Thermodynamic quantities related to hot and dense matter have been calculated as functions of proper time. Moreover, various initial conditions for the relaxation equations have been assumed to study their effects on above mentioned observables. A LHC QGP formation time of $\tau_0$ = 0.4 fm/c and temperature of T$_0$ = 500 MeV have been assumed.

Second order causal hydrodynamics in Eckart frame: using gradient expansion scheme

In the present work, we develop a causal theory of relativistic non-ideal fluids up to the second order in the Eckart frame using gradient expansion scheme. Keeping the spirit of Mueller–Israel–Stewart formalism, the general forms of bulk viscosity, shear viscosity tensor and the heat flow vector are presented. Since each of the flux quantities explicitly carry curvature terms, we show that our formalism finds application in astrophysics in particular in the strong gravity regime. We elucidate two such applications namely in viscous thick accretion disks also known as Polish doughnuts and in addressing non-rotating equilibrium configuration, like neutron stars.

Accurate Calculations of OH-Stretching Intensities with a Reduced-Dimensional Local Mode Model Including Eckart Axis Embedding.

Absolute OH- and OD-stretching transition intensities have been calculated for a series of alcohols (methanol, ethanol, 2-propanol, 1-propanol, and tert-butanol) with one-dimensional (1D) and three-dimensional (3D) local mode models. We compare the calculated intensities for the ΔvOH = 1-5 and ΔvOD = 1-3 transitions with experimental values. Potential energy and dipole moment surfaces are calculated at the CCSD(T)-F12a/VDZ-F12 level of theory. The 1D local mode model includes only the OH(D)-stretching mode, whereas the 3D local mode model also includes the CO-stretching and COH(D)-bending modes. We analyze the effect on vibrational intensities of using either a molecule-fixed Eckart frame or a space-fixed Cartesian frame. We find that both Eckart embedding and inclusion of the CO-stretching and COH(D)-bending modes in the local mode model are important for the OH/OD-stretching fundamental transition intensities, but have a minor effect on overtone intensities. The 3D reduced-dimensional local model, when combined with coupled cluster surfaces, accurately predicts OH/OD-stretching transition intensities and wavenumbers, for all alcohols included in this work.

Landau and Eckart frames for relativistic fluids in nuclear collisions

The quark matter created in relativistic nuclear collisions is interpreted as a nearly-perfect fluid. The recent efforts to explore its finite-density properties in the beam energy scan programs motivate one to revisit the issue of the local rest frame fixing in off-equilibrium hydrodynamics. I first investigate full second-order relativistic hydrodynamics in the Landau and the Eckart frames. Then numerical hydrodynamic simulations are performed to elucidate the effect of frame choice on flow observables in relativistic nuclear collisions. The results indicate that the flow can differ in the Landau and the Eckart frames but charged particle and net baryon rapidity distributions are mostly frame independent when off-equilibrium kinetic freeze-out is considered.

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis.

Two efficient methods, the Eckart frame algorithm and the multiorder derivative algorithm, for vibrational frequency calculation directly based on the raw data of atomic trajectory from the state-of-the-art first-principles molecular dynamics simulation are presented. The Eckart frame approach is robust to retrieve the full set of anharmonic fundamental frequencies of any molecule from the atomic trajectory for a sufficiently long molecular dynamics simulation at a temperature close to 0 K. In addition to the fundamental vibrational frequencies, the multiorder derivative approach is universal for the calculations of vibrational frequencies based on the molecular dynamics result in a wide range of temperatures. The accuracy, efficiency, and applicability of these two methods are demonstrated through several successful examples in calculating the anharmonic fundamental vibrational frequencies of methane, ethylene, water, and cyclobutadiene.

Rotation Dynamics of Star Block Copolymers under Shear Flow.

Star block-copolymers (SBCs) are macromolecules formed by a number of diblock copolymers anchored to a common central core, being the internal monomers solvophilic and the end monomers solvophobic. Recent studies have demonstrated that SBCs constitute self-assembling building blocks with specific softness, functionalization, shape and flexibility. Depending on different physical and chemical parameters, the SBCs can behave as flexible patchy particles. In this paper, we study the rotational dynamics of isolated SBCs using a hybrid mesoscale simulation technique. We compare three different approaches to analyze the dynamics: the laboratory frame, the non-inertial Eckart’s frame and a geometrical approximation relating the conformation of the SBC to the velocity profile of the solvent. We find that the geometrical approach is adequate when dealing with very soft systems, while in the opposite extreme, the dynamics is best explained using the laboratory frame. On the other hand, the Eckart frame is found to be very general and to reproduced well both extreme cases. We also compare the rotational frequency and the kinetic energy with the definitions of the angular momentum and inertia tensor from recent publications.

A New BGK Model for Relativistic Kinetic Theory of Monatomic and Polyatomic Gases

We propose a possible generalization of the BGK collisional term in the relativistic kinetic theory and we compare our model with previous ones. The present model has the advantage in that it satisfies the conservation of particle number, energy-momentum and the H-theorem in the Eckart frame without constraints on particular local equilibrium state. In the last part of the paper we extend the model to include also the polyatomic gas.

Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem.

Quantum mechanical calculations of ro-vibrational energies of CH4, CHD3, CH3D, and CH3F were made with two different numerical approaches. Both use polyspherical coordinates. The computed energy levels agree, confirming the accuracy of the methods. In the first approach, for all the molecules, the coordinates are defined using three Radau vectors for the CH3 subsystem and a Jacobi vector between the remaining atom and the centre of mass of CH3. Euler angles specifying the orientation of a frame attached to CH3 with respect to a frame attached to the Jacobi vector are used as vibrational coordinates. A direct product potential-optimized discrete variable vibrational basis is used to build a Hamiltonian matrix. Ro-vibrational energies are computed using a re-started Arnoldi eigensolver. In the second approach, the coordinates are the spherical coordinates associated with four Radau vectors or three Radau vectors and a Jacobi vector, and the frame is an Eckart frame. Vibrational basis functions are products of contracted stretch and bend functions, and eigenvalues are computed with the Lanczos algorithm. For CH4, CHD3, and CH3D, we report the first J > 0 energy levels computed on the Wang-Carrington potential energy surface [X.-G. Wang and T. Carrington, J. Chem. Phys. 141(15), 154106 (2014)]. For CH3F, the potential energy surface of Zhao et al. [J. Chem. Phys. 144, 204302 (2016)] was used. All the results are in good agreement with experimental data.

Eckart ro-vibrational Hamiltonians via the gateway Hamilton operator: Theory and practice.

Recently, a general expression for Eckart-frame Hamilton operators has been obtained by the gateway Hamiltonian method [V. Szalay, J. Chem. Phys. 142, 174107 (2015) and V. Szalay, J. Chem. Phys. 143, 064104 (2015)]. The kinetic energy operator in this general Hamiltonian is nearly identical to that of the Eckart-Watson operator even when curvilinear vibrational coordinates are employed. Its different realizations correspond to different methods of calculating Eckart displacements. There are at least two different methods for calculating such displacements: rotation and projection. In this communication, the application of Eckart Hamiltonian operators constructed by rotation and projection, respectively, is numerically demonstrated in calculating vibrational energy levels. The numerical examples confirm that there is no need for rotation to construct an Eckart ro-vibrational Hamiltonian. The application of the gateway method is advantageous even when rotation is used since it obviates the need for differentiation of the matrix rotating into the Eckart frame. Simple geometrical arguments explain that there are infinitely many different methods for calculating Eckart displacements. The geometrical picture also suggests that a unique Eckart displacement vector may be defined as the shortest (mass-weighted) Eckart displacement vector among Eckart displacement vectors corresponding to configurations related by rotation. Its length, as shown analytically and demonstrated by numerical examples, is equal to or less than that of the Eckart displacement vector one can obtain by rotation to the Eckart frame.