Related papers: Predicting the thermodynamics by using state-depen…
Density (or state) dependent pair potentials arise naturally from coarse-graining procedures in many areas of condensed matter science. However, correctly using them to calculate physical properties of interest is subtle and cannot be…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
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…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We focus on finding a coarse grained description able to reproduce the thermodynamic behavior of a molecular system by using mesoparticles representing several molecules. Interactions between mesoparticles are modelled by an interparticle…
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping…
Electrostatic interactions between macroions largely govern the equilibrium thermodynamic and dynamical properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions. Predicting the properties of such complex,…
Shedding a new light in the coarse-graining scenario, in this contribution we came up with different necessary and sufficient conditions for the existence of a well-defined coarse-grained state. For doing so, we had to break apart with the…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
In recent papers, we have argued that kinetically constrained coarse grained models can be applied to understand dynamic properties of glass forming materials, and we have used this approach in various applications that appear to validate…
We present recent results on coarse-graining techniques for thermodynamic quantities (canonical averages) and dynamical quantities (averages of path functionals over solutions of overdamped Langevin equations). The question is how to obtain…
A thermodynamics for systems at a stationary states is formulated. It is based upon the assumption of the existence of local equilibrium in phase space which enables one to interpret the probability density ans its conjugated nonequilibrium…
We systematically derive an exact coarse-grained description for interacting particles with thermodynamically consistent stochastic dynamics, applicable across different observation scales, the mesoscopic and the macroscopic. We implement…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…