Statistical mechanics of the GENERIC framework under external forcing.

The General Equation for Non-Equilibrium Reversible Irreversible Coupling (generic) framework provides a thermodynamically consistent approach to describe the evolution of coarse-grained variables. This framework states that Markovian dynamic equations governing the evolution of coarse-grained variables have a universal structure that ensures energy conservation (first law) and entropy increase (second law). However, the presence of external time-dependent forces can break the energy conservation law, requiring modifications to the framework's structure. To address this issue, we start from a rigorous and exact transport equation for the average of a set of coarse-grained variables derived from a projection operator technique in the presence of external forces. Under the Markovian approximation, this approach provides the statistical mechanics underpinning of the generic framework under external forcing conditions. By doing so, we can account for the effects of external forcing on the system's evolution while ensuring thermodynamic consistency.

Non-local viscosity from the Green-Kubo formula.

We study through MD simulations the correlation matrix of the discrete transverse momentum density field in real space for an unconfined Lennard-Jones fluid at equilibrium. Mori theory predicts this correlation under the Markovian approximation from the knowledge of the non-local shear viscosity matrix, which is given in terms of a Green-Kubo formula. However, the running Green-Kubo integral for the non-local shear viscosity does not have a plateau. By using a recently proposed correction for the Green-Kubo formula that eliminates the plateau problem [Español et al., Phys. Rev. E 99, 022126 (2019)], we unambiguously obtain the actual non-local shear viscosity. The resulting Markovian equation, being local in time, is not valid for very short times. We observe that the Markovian equation with non-local viscosity gives excellent predictions for the correlation matrix from a time at which the correlation is around 80% of its initial value. A local in space approximation for the viscosity gives accurate results only after the correlation has decayed to 40% of its initial value.

Microscopic Slip Boundary Conditions in Unsteady Fluid Flows.

An algebraic tail in the Green-Kubo integral for the solid-fluid friction coefficient hampers its use in the determination of the slip length. A simple theory for discrete nonlocal hydrodynamics near parallel solid walls with extended friction forces is given. We explain the origin of the algebraic tail and give a solution of the plateau problem in the Green-Kubo expressions. We derive the slip boundary condition with a microscopic expression for the slip length and the hydrodynamic wall position, and assess it through simulations of an unsteady plug flow.

Boundary conditions derived from a microscopic theory of hydrodynamics near solids.

The theory of nonlocal isothermal hydrodynamics near a solid object derived microscopically in the study by Camargo et al. [J. Chem. Phys. 148, 064107 (2018)] is considered under the conditions that the flow fields are of macroscopic character. We show that in the limit of macroscopic flows, a simple pillbox argument implies that the reversible and irreversible forces that the solid exerts on the fluid can be represented in terms of boundary conditions. In this way, boundary conditions are derived from the underlying microscopic dynamics of the fluid-solid system. These boundary conditions are the impenetrability condition and the Navier slip boundary condition. The Green-Kubo transport coefficients associated with the irreversible forces that the solid exert on the fluid appear naturally in the slip length. The microscopic expression for the slip length thus obtained is shown to coincide with the one provided originally by Bocquet and Barrat [Phys. Rev. E 49, 3079 (1994)].

Nanoscale hydrodynamics near solids.

Density Functional Theory (DFT) is a successful and well-established theory for the study of the structure of simple and complex fluids at equilibrium. The theory has been generalized to dynamical situations when the underlying dynamics is diffusive as in, for example, colloidal systems. However, there is no such a clear foundation for Dynamic DFT (DDFT) for the case of simple fluids in contact with solid walls. In this work, we derive DDFT for simple fluids by including not only the mass density field but also the momentum density field of the fluid. The standard projection operator method based on the Kawasaki-Gunton operator is used for deriving the equations for the average value of these fields. The solid is described as featureless under the assumption that all the internal degrees of freedom of the solid relax much faster than those of the fluid (solid elasticity is irrelevant). The fluid moves according to a set of non-local hydrodynamic equations that include explicitly the forces due to the solid. These forces are of two types, reversible forces emerging from the free energy density functional, and accounting for impenetrability of the solid, and irreversible forces that involve the velocity of both the fluid and the solid. These forces are localized in the vicinity of the solid surface. The resulting hydrodynamic equations should allow one to study dynamical regimes of simple fluids in contact with solid objects in isothermal situations.

The entropy of a complex molecule.

Entropy is a central concept in the theory of coarse-graining. Through Einstein's formula, it provides the equilibrium probability distribution of the coarse-grained variables used to describe the system of interest. We study with molecular dynamics simulations the equilibrium probability distribution of thermal blobs representing at a coarse-grained level star polymer molecules in melt. Thermal blobs are characterized by the positions and momenta of the centers of mass, and internal energies of the molecules. We show that the entropy of the level of description of thermal blobs can be very well approximated as the sum of the thermodynamic entropy of each single molecule considered as isolated thermodynamic systems. The entropy of a single molecule depends on the intrinsic energy, involving only contributions from the atoms that make the molecule and not from the interactions with atoms of other molecules.

Perspective: Dissipative particle dynamics.

Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field. We summarize some recent advances and suggest avenues for future developments.

Energy-conserving coarse-graining of complex molecules.

Coarse-graining (CG) of complex molecules is a method to reach time scales that would be impossible to access through brute force molecular simulations. In this paper, we formulate a coarse-grained model for complex molecules using first principles caculations that ensures energy conservation. Each molecule is described in a coarse way by a thermal blob characterized by the position and momentum of the center of mass of the molecule, together with its internal energy as an additional degree of freedom. This level of description gives rise to an entropy-based framework instead of the usual one based on the configurational free energy (i.e. potential of mean force). The resulting dynamic equations, which account for an appropriate description of heat transfer at the coarse-grained level, have the structure of the dissipative particle dynamics with energy conservation (DPDE) model but with a clear microscopic underpinning. Under suitable approximations, we provide explicit microscopic expressions for each component (entropy, mean force, friction and conductivity coefficients) appearing in the coarse-grained model. These quantities can be computed directly using MD simulations. The proposed non-isothermal coarse-grained model is thermodynamically consistent and opens up a first principles CG strategy for the study of energy transport issues that are not accessible using current isothermal models.

Coupling a nano-particle with isothermal fluctuating hydrodynamics: Coarse-graining from microscopic to mesoscopic dynamics.

We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our "bottom-up" and previous "top-down" approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a "linear for spiky" weak approximation which replaces microscopic "fields" with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics simulations as input to a FEM fluctuating hydrodynamic solver.

Finite element discretization of non-linear diffusion equations with thermal fluctuations.

We present a finite element discretization of a non-linear diffusion equation used in the field of critical phenomena and, more recently, in the context of dynamic density functional theory. The discretized equation preserves the structure of the continuum equation. Specifically, it conserves the total number of particles and fulfills an H-theorem as the original partial differential equation. The discretization proposed suggests a particular definition of the discrete hydrodynamic variables in microscopic terms. These variables are then used to obtain, with the theory of coarse-graining, their dynamic equations for both averages and fluctuations. The hydrodynamic variables defined in this way lead to microscopically derived hydrodynamic equations that have a natural interpretation in terms of discretization of continuum equations. Also, the theory of coarse-graining allows to discuss the introduction of thermal fluctuations in a physically sensible way. The methodology proposed for the introduction of thermal fluctuations in finite element methods is general and valid for both regular and irregular grids in arbitrary dimensions. We focus here on simulations of the Ginzburg-Landau free energy functional using both regular and irregular 1D grids. Convergence of the numerical results is obtained for the static and dynamic structure factors as the resolution of the grid is increased.

Hamiltonian adaptive resolution simulation for molecular liquids.

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well-defined statistical ensembles can be generated making use of all standard molecular dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

Monte carlo adaptive resolution simulation of multicomponent molecular liquids.

Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The nonmatching properties of high- and low-resolution models, however, lead to thermodynamic imbalances between the system's subdomains. Such inhomogeneities can be healed by appropriate compensation forces, whose calculation requires nontrivial iterative procedures. In this work we employ the recently developed Hamiltonian adaptive resolution simulation method to perform Monte Carlo simulations of a binary mixture, and propose an efficient scheme, based on Kirkwood thermodynamic integration, to regulate the thermodynamic balance of multicomponent systems.

Functional thermo-dynamics: a generalization of dynamic density functional theory to non-isothermal situations.

We present a generalization of Density Functional Theory (DFT) to non-equilibrium non-isothermal situations. By using the original approach set forth by Gibbs in his consideration of Macroscopic Thermodynamics (MT), we consider a Functional Thermo-Dynamics (FTD) description based on the density field and the energy density field. A crucial ingredient of the theory is an entropy functional, which is a concave functional. Therefore, there is a one to one connection between the density and energy fields with the conjugate thermodynamic fields. The connection between the three levels of description (MT, DFT, FTD) is clarified through a bridge theorem that relates the entropy of different levels of description and that constitutes a generalization of Mermin's theorem to arbitrary levels of description whose relevant variables are connected linearly. Although the FTD level of description does not provide any new information about averages and correlations at equilibrium, it is a crucial ingredient for the dynamics in non-equilibrium states. We obtain with the technique of projection operators the set of dynamic equations that describe the evolution of the density and energy density fields from an initial non-equilibrium state towards equilibrium. These equations generalize time dependent density functional theory to non-isothermal situations. We also present an explicit model for the entropy functional for hard spheres.

Markovian dissipative coarse grained molecular dynamics for a simple 2D graphene model.

Based upon a finite-element "coarse-grained molecular dynamics" (CGMD) procedure, as applied to a simple atomistic 2D model of graphene, we formulate a new coarse-grained model for graphene mechanics explicitly accounting for dissipative effects. It is shown that, within the Mori-projection operator formalism, the reversible part of the dynamics is equivalent to the finite temperature CGMD-equations of motion, and that dissipative contributions to CGMD can also be included within the Mori formalism. The CGMD nodal momenta in the present graphene model display clear non-Markovian behavior, a property that can be ascribed to the fact that the CGMD-weighting function suppresses high-frequency modes more effectively than, e.g., a simple center of mass (COM) based CG procedure. The present coarse-grained graphene model is also shown to reproduce the short time behavior of the momentum correlation functions more accurately than COM-variables and it is less dissipative than COM-CG. Finally, we find that, while the intermediate time scale represented directly by the CGMD variables shows a clear non-Markovian dynamics, the macroscopic dynamics of normal modes can be approximated by a Markovian dissipation, with friction coefficients scaling like the square of the wave vector. This opens the way to the development of a CGMD model capable of describing the correct long time behavior of such macroscopic normal modes.

Obtaining fully dynamic coarse-grained models from MD.

We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected.

Coarse-graining Brownian motion: from particles to a discrete diffusion equation.

We study the process of coarse-graining in a simple model of diffusion of Brownian particles. At a detailed level of description, the system is governed by a Brownian dynamics of non-interacting particles. The coarse-level is described by discrete concentration variables defined in terms of Delaunay cells. These coarse variables obey a stochastic differential equation that can be understood as a discrete version of a diffusion equation. We study different models for the two basic building blocks of this equation which are the free energy function and the diffusion matrix. The free energy function is shown to be non-additive due to the overlapping of cells in the Delaunay construction. The diffusion matrix is state dependent in principle, but for near-equilibrium situations it is shown that it may be safely evaluated at the equilibrium value of the concentration field.

Bottom-up coarse-graining of a simple graphene model: the blob picture.

The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined.

Derivation of dynamical density functional theory using the projection operator technique.

Density functional theory is a particular case of a general theory of conjugate variables that serves as the basis of the projection operator technique. By using this technique we derive a general dynamical version of density functional theory which involves a generalized diffusion tensor. The diffusion tensor is given by a Green-Kubo expression. For Brownian dynamics of dilute colloidal suspensions, the standard dynamical density functional theory is recovered.

On the definition of discrete hydrodynamic variables.

The Green-Kubo formula for discrete hydrodynamic variables involves information about not only the fluid transport coefficients but also about discrete versions of the differential operators that govern the evolution of the discrete variables. This gives an intimate connection between discretization procedures in fluid dynamics and coarse-graining procedures used to obtain hydrodynamic behavior of molecular fluids. We observed that a natural definition of discrete hydrodynamic variables in terms of Voronoi cells leads to a Green-Kubo formula which is divergent, rendering the full coarse-graining strategy useless. In order to understand this subtle issue, in the present paper we consider the coarse graining of noninteracting Brownian particles. The discrete hydrodynamic variable for this problem is the number of particles within Voronoi cells. Thanks to the simplicity of the model we spot the origin of the singular behavior of the correlation functions. We offer an alternative definition, based on the concept of a Delaunay cell that behaves properly, suggesting the use of the Delaunay construction for the coarse graining of molecular fluids at the discrete hydrodynamic level.

Consistent scaling of thermal fluctuations in smoothed dissipative particle dynamics.

Dissipative particle dynamics (DPD) as a model of fluid particles suffers from the problem that it has no physical scale associated with the particles. Therefore, a DPD simulation requires an ambiguous fine-tuning of the model parameters with the physical parameters. A corrected version of DPD that does not suffer from this problem is smoothed dissipative particle dynamics (SDPD) [P. Espanol and M. Revenga, Phys. Rev. E 67, 026705 (2003)]. SDPD is, in fact, a version of the well-known smoothed particle hydrodynamics method, albeit with the proper inclusion of thermal fluctuations. Here, we show that SDPD produces the proper scaling of the fluctuations as the resolution of the simulation is varied. This is investigated in two problems: the Brownian motion of a spherical colloidal particle and a polymer molecule in suspension.