At first glance the definition of mass and momentum appears to be uniquely defined. We show here, however, that this certainty can be misleading for many coarse grained systems. We show that particularly the fluctuating properties of common definitions of momentum in coarse grained methods like lattice gas and lattice Boltzmann do not agree with a fundamental definition of momentum. In the case of lattice gases, the definition of momentum will even disagree in the limit of large wavelength. For short times we can give analytical representations for the distribution of different momentum measures and thereby give a full account of these differences.
By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to critical slowing down, an extremal autocorrelation time can also be considered as an indicator for the collapse transition that helps to locate the transition point. This is particularly useful for finite systems, where response quantities such as the specific heat do not necessarily exhibit clear indications for pronounced thermal activity.
While linear response theory, manifested by the fluctuation dissipation theorem, can be applied at any level of coarse graining, nonlinear response theory is fundamentally of microscopic nature. For perturbations of equilibrium systems, we develop an exact theoretical framework for analyzing the nonlinear (second order) response of coarse grained observables to time-dependent perturbations, using a path-integral formalism. The resulting expressions involve correlations of the observable with coarse grained path weights. The time symmetric part of these weights depends on the paths and perturba…
We show an interesting connexion between the coarse-grained distribution function arising in the theory of violent relaxation for collisionless stellar systems (Lynden-Bell 1967) and the notion of superstatistics introduced recently by Beck & Cohen (2003). We also discuss the analogies and differences between the statistical equilibrium state of a multi-components self-gravitating system and the metaequilibrium state of a collisionless stellar system. Finally, we stress the important distinction between mixing entropies, generalized entropies, H-functions, generalized mixing entropies and rela…
We propose a degree-based coarse graining approach that not just accelerates the evaluation of dynamics on complex networks, but also satisfies the consistency conditions for both equilibrium statistical distributions and nonequilibrium dynamical flows. For the Ising model and susceptible-infected-susceptible epidemic model, we introduce these required conditions explicitly and further prove that they are satisfied by our coarse-grained network construction within the annealed network approximation. Finally, we numerically show that the phase transitions and fluctuations on the coarse-grained …
We propose a novel and systematic method for coarse-graining oscillator networks described by phase equations. Our coarse-graining method enables us to obtain the closed coarse-grained equations for a few effective eigenmodes, which is based on the eigenvalue problem of the linearized system around the phase-locked solution and a nonlinear transformation. We demonstrate our method by applying it to oscillator dynamics on a random graph, which exhibits a saddle-node bifurcation at the bifurcation point.
We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme …
We introduce a coarse-grained model for atomic glass formers. Its elements are physically motivated local microscopic dynamical rules parameterized by observables. Results of the model are established and used to interpret the measured behaviors of supercooled fluids approaching glass transitions. The model predicts the presence of a crossover from hierarchical super-Arrhenius dynamics at short length scales to diffusive Arrhenius dynamics at large length scales. This prediction distinguishes our model from other theories of glass formers and can be tested by experiment.
Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master Equation that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We show that the corresponding coarse-grained entropy production contains information on microscopic currents that are not captured by the Fokker-Planck equation and thus cannot be deduced from it. We study a discrete-state and a continuous-state system, deriving in both the cases an analytical expression for the coarse-graining corrections to the entropy product…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how h…
Nonlinear response theory, in contrast to linear cases, involves (dynamical) details, and this makes application to many body systems challenging. From the microscopic starting point we obtain an exact response theory for a small number of coarse grained degrees of freedom. With it, an extrapolation scheme uses near-equilibrium measurements to predict far from equilibrium properties (here, second order responses). Because it does not involve system details, this approach can be applied to many body systems. It is illustrated in a four state model and in the near critical Ising model.
The problem of calculating the rate of mutual information between two coarse-grained variables that together specify a continuous time Markov process is addressed. As a main obstacle, the coarse-grained variables are in general non-Markovian, therefore, an expression for their Shannon entropy rates in terms of the stationary probability distribution is not known. A numerical method to estimate the Shannon entropy rate of continuous time hidden-Markov processes from a single time series is developed. With this method the rate of mutual information can be determined numerically. Moreover, an ana…
Understanding Dynamics in Coarse-Grained Models: IV. Connection of Fine-Grained and Coarse-Grained Dynamics with the Stokes-Einstein and Stokes-Einstein-Debye Relations
Coarse-grained models have proven helpful for simulating complex systems over long timescales to provide molecular insights into various processes. Methodologies for systematic parameterization of the underlying energy function, or force field that describes the interactions among different components of the system are of great interest for ensuring simulation accuracy. We present a new method, potential contrasting, to enable efficient learning of force fields that can accurately reproduce the conformational distribution produced with all-atom simulations. Potential contrasting generalizes th…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been developed. In this letter, we present an approach that leads to a dynamics for such coarse-grained models. This allows us to obtain temperature-dependent and transport properties. Renormalization group theory is used to create new local potentials model between nodes, within the approximation of local thermodynamical equilibrium. Assuming that these potentia…
A new class of patterns for multiplex networks is studied, which consists in a collection of different homogeneous states each referred to a distinct layer. The associated stability diagram exhibits a tricritical point, as a function of the inter-layer diffusion coefficients. The coarse-grained patterns made of alternating homogenous layers, are dynamically selected via non homogeneous perturbations superposed to the underlying, globally homogeneous, fixed point and by properly modulating the coupling strength between layers. Furthermore, layer-homogenous fixed points can turn unstable followi…
Equations of motion for the microscopic number density $\hatρ({\bf x},t)$ and the momentum density $\hat{\bf g}({\bf x},t)$ of a fluid have been obtained in the past from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a syste…
An approximate treatment of exchange in finite-temperature path integral Monte Carlo simulations for fermions has been proposed. In this method, some of the fine details of density matrix due to permutations have been smoothed over or averaged out by using the coarse-grained approximation. The practical usefulness of the method is tested for interacting fermions in a three dimensional harmonic well. The results show that, the present method not only reduces the sign fluctuation of the density matrix, but also avoid the fermion system collapsing into boson system at low temperatures. The method…
We describe a general simulation scheme for assessing the thermodynamic consequences of neglecting many-body effects in coarse-grained models of complex fluids. The method exploits the fact that the asymptote of a simple-to-measure structural function provides direct estimates of virial coefficients. Comparing the virial coefficients of an atomistically detailed system with those of a coarse-grained version described by pair potentials, permits the role of many-body effects to be quantified. The approach is applied to two models: (i) a size-asymmetrical colloid-polymer mixture, and (ii) a solu…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle formation. The procedure hinges on the (expected) evolution of a few slow, coarse-grained mesoscopic observables of the MC simulation, and on (computational) time scale separation between these and the remaining "slaved", fast variables. Short bursts of appropriately initialized atomistic simulation are used to estimate the (coarse-grained, deterministic) local dynam…
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that evolves in time. This is a challenging task. As a preparation to the topic, we recall equilibrium coarse-graining methods, both theoretical and numerical, such as projection operator formalisms, united atom simulations, numerical reconstruction of memory and Markov State Modelling. Then we review recent developments in theoretical approaches to the non-equi…
Integral equation theory is applied to a coarse-grained model of water to study potential of mean force between hydrophobic solutes. Theory is shown to be in good agreement with the available simulation data for methane-methane and fullerene-fullerene potential of mean force in water; the potential of mean force is also decomposed into its entropic and enthalpic contributions. Mode coupling theory is employed to compute self-diffusion coefficient of water, as well as diffusion coefficient of a dilute hydrophobic solute; good agreement with molecular dynamics simulation results is found.
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special attention to model development and computational techniques. Applications of coarse-grained models to chan…
Using concepts from integral geometry, we propose a definition for a local coarse-grained curvature tensor that is well-defined on polygonal surfaces. This coarse-grained curvature tensor shows fast convergence to the curvature tensor of smooth surfaces, capturing with accuracy not only the principal curvatures but also the principal directions of curvature. Thanks to the additivity of the integrated curvature tensor, coarse-graining procedures can be implemented to compute it over arbitrary patches of polygons. When computed for a closed surface, the integrated curvature tensor is identical t…
Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units (CGU) as connectivity patterns which can serve as the nodes of a coarse-grained network, and present algorithms to detect them. We use this approach to systematically reverse-engineer electronic circuits, forming understandable high-level maps from incomprehensible transistor wiring: first, a coarse-grained version in which each node is a gate made of several trans…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are modeled on a mesh in a formulation that generalizes conventional finite element modeling (FEM) of continuum elasticity. CGMD is derived solely from the MD model, however, and has no continuum parameters. As a result, it provides a coupling that is smooth and provides control of errors that arise at the coupling between the atomistic and coarse-grained regions. In…
We consider an open quantum system for which only a subset of all possible transitions are accessible, while the remaining ones are hidden from direct observation. Using a modification of the notion of quantum jump trajectories we introduce the coarse-grained hidden entropy, which quantifies the entropy production in the hidden subsystem conditioned on our observations of the visible part. The entropy production consisting of the sum of visible and coarse-grained hidden entropy is shown to satisfy an integral fluctuations theorem. Depending on the nature of the continuously occurring measureme…
Recent Monte Carlo simulations (A. G. Moreira and R. R. Netz: Eur. Phys. J. E {\bf 8} (2002) 33) in the strong Coulomb coupling regime suggest strange counterion electrostatics unlike the Poisson-Boltzmann picture: when counterion-counterion repulsive interactions are much larger than counterion--macroion attraction, the coarse-grained counterion distribution around a macroion is determined only by the latter, and the former is irrelevant. Here, we offer an explanation for the apparently paradoxical electrostatics by mathematically manipulating the strong coupling limit.
A first-principle multiscale modeling approach is presented, which is derived from the solution of the Ornstein-Zernike equation for the coarse-grained representation of polymer liquids. The approach is analytical, and for this reason is transferable. It is here applied to determine the structure of several polymeric systems, which have different parameter values, such as molecular length, monomeric structure, local flexibility, and thermodynamic conditions. When the pair distribution function obtained from this procedure is compared with the results from a full atomistic simulation, it shows …
We show how to implement stick boundary conditions for a spherical colloid in a solvent that is coarse-grained by the method of stochastic rotation dynamics. This allows us to measure colloidal rotational velocity auto-correlation functions by direct computer simulation. We find quantitative agreement with Enskog theory for short times and with hydrodynamic mode-coupling theory for longer times. For aqueous colloidal suspensions, the Enskog contribution to the rotational friction is larger than the hydrodynamic one when the colloidal radius drops below 35nm.
We present a theoretical framework to analyze the dynamics of gene expression with stochastic bursts. Beginning with an individual-based model which fully accounts for the messenger RNA (mRNA) and protein populations, we propose a novel expansion of the master equation for the joint process. The resulting coarse-grained model reduces the dimensionality of the system, describing only the protein population while fully accounting for the effects of discrete and fluctuating mRNA population. Closed form expressions for the stationary distribution of the protein population and mean first-passage ti…
We present an effective evolution equation for a coarse-grained distribution function of a long-range-interacting system preserving the symplectic structure of the non-collisional Boltzmann, or Vlasov, equation. We first derive a general form of such an equation based on symmetry considerations only. Then, we explicitly derive the equation for one-dimensional systems, finding that it has the form predicted on general grounds. Finally, we use such an equation to predict the dependence of the damping times on the coarse-graining scale and numerically check it for some one-dimensional models, inc…
We present a theoretical approach which maps polymer blends onto mixtures of soft-colloidal particles. The analytical mesoscale pair distribution functions reproduce well data from united atom molecular dynamics simulations of polyolefin mixtures without fitting parameters. The theory exactly recovers the analytical expressions for density and concentration fluctuation structure factors of soft colloidal mixtures (liquid alloys).
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized part…
We discuss a coarse-grained approach to the computation of rare events in the context of grand canonical Monte Carlo (GCMC) simulations of self-assembly of surfactant molecules into micelles. The basic assumption is that the {\it computational} system dynamics can be decomposed into two parts -- fast (noise) and slow (reaction coordinates) dynamics, so that the system can be described by an effective, coarse grained Fokker-Planck (FP) equation. While such an assumption may be valid in many circumstances, an explicit form of FP equation is not always available. In our computations we bypass the…
We introduce a coarse-grained description of the surface energy of a nematic liquid crystal. The thermal fluctuations of the nematic director close to the surface renormalize at macroscopic scales the bare surface potential in a temperature-dependent way. The angular dependence of the renormalized potential is dramatically smoothed, thus explaining the success of the Rapini-Papoular form. Close to the isotropic phase, the anchoring energy is strongly suppressed and the change of its shape allows for anchoring transitions. Our theory describes quantitatively the temperature dependence of the an…
Information-theoretical quantities such as statistical distinguishability typically result from optimisations over all conceivable observables. Physical theories, however, are not generally considered valid for all mathematically allowed measurements. For instance, quantum field theories are not meant to be correct or even consistent at arbitrarily small lengthscales. A general way of limiting such an optimisation to certain observables is to first coarse-grain the states by a quantum channel. We show how to calculate contractive quantum information metrics on coarse-grained equilibrium states…
Galilean invariance is a cornerstone of classical mechanics. It states that for closed systems the equations of motion of the microscopic degrees of freedom do not change under Galilean transformations to different inertial frames. However, the description of real world systems usually requires coarse-grained models integrating complex microscopic interactions indistinguishably as friction and stochastic forces, which intrinsically violate Galilean invariance. By studying the coarse-graining procedure in different frames, we show that alternative rules -- denoted as "weak Galilean invariance" …
We present two coarse-grained models of different levels of detail for the description of beta-sheet tapes obtained from equilibrium self-assembly of short rationally designed oligopeptides in solution. Here we only consider the case of the homopolymer oligopeptides with the identical sidegroups attached, in which the tapes have a helicoid surface with two equivalent sides. The influence of the chirality parameter on the geometrical characteristics, namely the diameter, inter-strand distance and pitch, of the tapes have been investigated. The two models are found to produceequivalent results s…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is represented by a single interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. This bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the DNA model to perform simulations of the self-assembly kinetics of DNA tet…
