Unique characterization of materials with memory

A material with memory typically has a set of many free energy functionals associated with it, all members of which yield the same constitutive relations. An alternative interpretation of this set is explored in the present work. Explicit formulae are derived for the free energy and total dissipation of an arbitrary material in the cases of step function and sinusoidal/exponential histories. Expressions for the fraction of stored and dissipated energy are deduced. Also, various formulae are given for discrete spectrum materials. For materials with relaxation function containing one decaying exponential, the associated Day functional is the physical free energy. For more general materials, we seek a best fit of the relaxation function with one decaying exponential to that chosen for the general case. The free energy, total dissipation and fractions of stored and dissipated energies relating to the Day material are derived for the various histories. Similar data, in the case of the general material, are explored for the minimum and maximum free energies and also for a centrally located free energy given in the literature. Various plots of aspects of this data, including comparisons between the behaviour for general and Day materials, are presented and discussed.

The Hencky medium with softening under isothermal and quasistatic deformation is considered. It is believed that volume deformation is not positive. In this case softening is characterized by the part of union curve with negative slope. For aforementioned conditions function of free energy is presented. For all stages of deformation in the space “volume deformation - intensity of shear’s deformation” level lines of the free energy are constructed. It is established that level lines are ellipses in hardening and function of free energy increases with distance from their centers, while in softening hyperbolas are level lines and function of free energy decreases with distance from their centers. Obtained results indirectly confirm the change in type of boundary value problem from elliptic to hyperbolic under material transition to the softening.

The aim of this work is to determine what free energy functionals are expressible as quadratic forms of the state functional \(I^t\) which is discussed in earlier papers. The single integral form is shown to include the functional \(\psi _F\) proposed a few years ago, and also a further category of functionals which are easily described but more complicated to construct. These latter examples exist only for certain types of materials. The double integral case is examined in detail, against the background of a new systematic approach developed recently for double integral quadratic forms in terms of strain history, which was used to uncover new free energy functionals. However, while, in principle, the same method should apply to free energies which can be given by quadratic forms in terms of \(I^t\), it emerges that this requirement is very restrictive; indeed, only the minimum free energy can be expressed in such a manner.

The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.

The free energy functions for electron transfer reactions in solution are explored using a previously developed microscopic simulation approach that provides a clear definition of these functions and the variable (the reaction coordinate) used as their argument. The issue of whether the curvatures of the two functions (which correspond to states with nonpolar and polar solutes) are different is given special attention. It is found, in contrast to some previous suggestions, that the curvatures of the two functions are quite similar, even when one would expect differences due to dielectric saturation effects, and that Marcus’ approximation (and, in fact, the linear response theory inherent in this approximation) provides a valid description of the solvent’s role in electron transfer reactions over a wide range of conditions. The present study demonstrates that direct simulations of the reactant and product states do not provide the data needed for determination of the free energy functions in high energy regions. On the other hand, a free energy perturbation approach developed in our early studies does allow one to obtain statistically significant data for these regions of high free energy. Inclusion of the solvent electronic polarizabilities in the potential results in a marked lowering of the solvent reorganization energy, but does not change the ratio of the curvatures of the free energy functions for the nonpolar and polar states. Finally, the effect of solvent tunneling is evaluated with the dispersed polaron method and shown to be rather small, and it is argued that the observed deviations from the classical Marcus theory in the inverted region are due to quantum mechanical tunneling associated with the solute vibrations, rather than to differences in the curvatures of the solvent free energy functions.

We develop a novel data-driven approach to the inverse problem of classical statistical mechanics: Given the experimental data on the collective motion of a classical many-body system, how does one characterize the free energy landscape of that system? By combining non-parametric Bayesian inference with physically motivated constraints, we develop an efficient learning algorithm that automates the construction of approximate free-energy functionals. In contrast to optimization-based machine learning approaches, which seek to minimize a cost function, the central idea of the proposed Bayesian inference is to propagate a set of prior assumptions through the model, derived from physical principles. The experimental data are used to probabilistically weigh the possible model predictions. This naturally leads to humanly interpretable algorithms with full uncertainty quantification of predictions. In our case, the output of the learning algorithm is a probability distribution over a family of free energy functionals, consistent with the observed particle data. We find that surprisingly small data samples contain sufficient information for inferring highly accurate analytic expressions of the underlying free-energy functionals, making our algorithm highly data efficient. In particular, we consider classical particle systems with excluded volume interactions, which are ubiquitous in nature, while being highly challenging in terms of free energy modeling. We validate our approach on the paradigmatic case of one-dimensional fluid and develop inference algorithms for the canonical and grand-canonical statistical-mechanical ensembles. Extensions to higher dimensional systems are conceptually straightforward, while standard coarse-graining techniques allow one to easily incorporate attractive interactions.

We study a phase-field variational model for the solvaiton of charged molecules with an implicit solvent. The solvation free-energy functional of all phase fields consists of the surface energy, solute excluded volume and solute-solvent van der Waals dispersion energy, and electrostatic free energy. The surface energy is defined by the van der Waals--Cahn--Hilliard functional with squared gradient and a double-well potential. The electrostatic part of free energy is defined through the electrostatic potential governed by the Poisson--Boltzmann equation in which the dielectric coefficient is defined through the underlying phase field. We prove the continuity of the electrostatics---its potential, free energy, and dielectric boundary force---with respect to the perturbation of dielectric boundary. We also prove the $\Gamma$-convergence of the phase-field free-energy functionals to their sharp-interface limit, and the equivalence of the convergence of total free energies to that of all individual parts of free energy. We finally prove the convergence of phase-field forces to their sharp-interface limit. Such forces are defined as the negative first variations of the free-energy functional; and arise from stress tensors. In particular, we obtain the force convergence for the van der Waals--Cahn--Hilliard functionals with minimal assumptions.

A combined isotropic and kinematic hardening model for the viscoplastic behavior of unidirectional fiber-reinforced composites is presented. Unidirectional composites are treated as transversely isotropic homogeneous media that harden with viscoplastic deformation. The formulation is based on the irreversible thermodynamics with internal variables, and the constitutive equations are derived from free energy and dissipation function. The combined isotropic and kinematic hardening model for transversely isotropic media can be reduced to pure isotropic hardening and kinematic hardening versions. Although the isotropic hardening model is similar to special cases of existing macromechanics models, it is furnished with an enhanced capability to describe the nonlinearity of the off-axis viscoplastic deformation of unidirectional composites. Validity of the proposed model is evaluated through comparisons between the predictions and observations for the rate-dependent nonlinear behavior of the unidirectional carbon fiber-reinforced composite AS4/PEEK under off-axis monotonic loading conditions.

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

Monte Carlo simulations are used to study the translocation of a polymer into and out of an ellipsoidal cavity through a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the number of bonds that have entered the cavity. To study polymer insertion, we consider the case of a driving force acting on monomers inside the pore, as well as monomer attraction to the cavity wall. We examine the changes to F(s) upon variation in the shape anisometry and volume of the cavity, the polymer length, and the strength of the interactions driving the insertion. For athermal systems, the free energy functions are analyzed using a scaling approach, where we treat the confined portion of the polymer to be in the semi-dilute regime. The free energy functions are used with the Fokker-Planck (FP) equation to calculate mean translocation times, as well as translocation time distributions. We find that both polymer ejection and insertion are faster for ellipsoidal cavities than for spherical cavities. The results are in qualitative agreement with those of a Langevin dynamics study in the case of ejection but not for insertion. The discrepancy is likely due to out-of-equilibrium conformational behaviour that is not accounted for in the FP approach.

Protein molecules in solution have a broad distribution of enthalpy states. A good approximation to the distribution function for enthalpy states can be calculated, using the maximum-entropy method, from the moments of the distribution that, in turn, are obtained from the experimental temperature dependence of the heat capacity. In the present paper, we show that the enthalpy probability distribution can then be formulated in terms of a free energy function that gives the free energy of the protein corresponding to a particular value of the enthalpy. By the location of the minima in this function, the free energy distribution graphically indicates the most probable values of the enthalpy for the protein. We find that the behavior of the free energy functions for proteins falls somewhere between two different cases: a two-state like function with two minima, the relative levels of the two states changing with temperature; and, a single-minimum function where the position of the minimum shifts to higher enthalpy values as the temperature is increased. We show that the temperature dependence of the free energy function can be expressed in terms of a central free energy distribution for a given, fixed temperature (which is most conveniently chosen as the temperature of the maximum in the heat capacity). The nature of this central free energy function for a given protein thus yields all of the thermodynamic behavior of that protein over the temperature range of the denaturation process.

In many aspects, elastomers and soft biological tissues exhibit similar mechanical properties such as a pronounced nonlinear stress–strain relation and a viscoelastic response to external loads. Consequently, many models use the same rheological framework and material functions to capture their behavior. The viscosity function is thereby often assumed to be constant and the corresponding free energy function follows that one of the long-term equilibrium response. This work questions this assumption and presents a detailed study on non-Newtonian viscosity functions for elastomers and brain tissues. The viscosity functions are paired with several commonly used free energy functions and fitted to two different types of elastomers and brain tissues in cyclic and relaxation experiments, respectively. Having identified suitable viscosity and free energy functions for the different materials, numerical aspects of viscoelasticity are addressed. From the multiplicative decomposition of the deformation gradient and ensuring a non-negative dissipation rate, four equivalent viscoelasticity formulations are derived that employ different internal variables. Using an implicit exponential map as time integration scheme, the numerical behavior of these four formulations are compared among each other and numerically robust candidates are identified. The fitting results demonstrate that non-Newtonian viscosity functions significantly enhance the fitting quality. It is shown that the choice of a viscosity function is even more important than the choice of a free energy function and the classical neo-Hooke approach is often a sufficient choice. Furthermore, the numerical investigations suggest the superiority of two of the four viscoelasticity formulations, especially when complex finite element simulations are to be conducted.

The mechanical behavior of monolithic cementitious materials is known to be significantly affected by their granular nature. This paper describes an approach to incorporate the effects of granularity for cementitious material based upon the granular micromechanics paradigm and thermomechanics. As a result, macro-scale constitutive equations that utilize grain-scale force–displacement relationships have been derived. In this derivation, the connections between grain-scale free energy and dissipation and the macro-scale behavior are established based upon the thermomechanics framework. Expression for Cauchy stress tensor is obtained in terms of the free energy of grain-pair interactions. In addition, the free energy and dissipation potential of grain-pair interactions are used to find a grain-scale Clausius–Duhem type inequality. Thus, inter-granular constitutive equations are obtained in the usual manner with the exception that these are based upon simple physically motivated free energy and dissipation functions formulated in terms of grain-pair interactions. The derived model is used to simulate a wide variety of experimental tests that have been reported in the literature to evaluate material response under multi-axial conditions. The results are analyzed with the aim to reveal the connections between grain-scale mechanisms and the macro-scale behavior.

Calculating the equilibrium composition of systems under given conditions (usually, temperature and pressure) is a core in the majority of the existing computer models of geochemical processes. Recently, Shvarov [1] investigated the thermodynamic consistency of the models of nonideal aqueous solutions that are used in geochemical calculations. He distinguished necessary and sufficient conditions for the thermodynamic consistency of the physicochemical models of real (nonideal) solutions and presented particular examples of errors appearing when these criteria are not met. In addition, Shvarov [1] claimed that the models that are currently used for concentrated electrolyte solutions are thermodynamically inconsistent. Such a pessimistic conclusion is related to a large extent to the fact that Shvarov’s [1] analysis was limited to the Debye‐Huckel model, which is applicable to diluted aqueous solutions, and its empirical modifications aimed at extending to concentrated aqueous solutions. Indeed, such models are thermodynamically inconsistent. However, models have been developed allowing adequate description of the behavior of concentrated aqueous solutions. One of them is the wellknown Pitzer model [2, 3] proposed for the description of the properties of dense electrolyte solutions in a wide range of temperatures, pressures, and compositions. The Pitzer model was developed on the basis of the Gibbs method and is, consequently, thermodynamically sound. If correct numerical algorithms are employed, the Pitzer model allows for the calculation of chemical equilibria in water‐ salt systems within a wide concentration range. The Pitzer model is an example of the rigorous statistical mechanical description of a multicomponent fluid system and the calculation of free energy by the Gibbs method. The derivation of an expression for free energy in the Pitzer model was described in detail in [2, 3], and only its basic principles are shortly discussed here. It is based on the approach developed by McMillan and Mayer [4], who described interactions between dissolved species within the mean field approximation and ignored the detailed description of interactions between individual particles. It should be emphasized that these approximations concern interactions between particles, i.e., a microscopic Hamiltonian. The free energy function is further derived in accordance with the statistical method of Gibbs using the methods of group expansion of Mayer [5, 6] and divergence elimination [6, 7] for the calculation of the configuration integrals of the long-range potentials of electrostatic interactions. Eventually, the excess Gibbs free energy of solution is given in the Pitzer model, after transition from volume concentrations to molalities, as [2]

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors