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In systems biology effective models are widely used due to the complexity of biological system. They result from a coarse-graining process which employs specific assumptions. Frequently one does not start with a model taking all details…
We study swelling and structural properties of ionic microgel suspensions within a comprehensive coarse-grained model that combines the polymeric and colloidal natures of microgels as permeable, compressible, charged spheres governed by…
Pair potentials that are bounded at the origin provide an accurate description of the effective interaction for many systems of dissolved soft macromolecules (e.g., flexible dendrimers). Using numerical free-energy calculations, we…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
In this brief note, the configurational density of states of a system of particles interacting via power-law pair potentials is computed exactly. The result is consistent with a constant microcanonical heat capacity. The well-known form of…
Any interface boundary in an equilibrium system of Coulomb particles is accompanied by the existence of a finite difference in the average electrostatic potential through this boundary. The discussed interface potential drop is a…
We develop a modified "two-state" model with Gaussian widths for the site energies of both ground and excited states, consistent with expectations for a disordered system. The thermodynamic properties of the system are analyzed in…
On the basis of the extended classical elasticity theory, we propose universal semi-empirical analytical expressions for the energy and the equation of state for poly-crystalline solids. The validation of the relations has been made by…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We show that a mesoscopic coarse-grained dynamics model which incorporates the transient potential can be formally derived from an underlying microscopic dynamics model. As a microscopic dynamics model, we employ the overdamped Langevin…
For a given thermodynamic system, and a given choice of coarse-grained state variables, the knowledge of a force-flux constitutive law is the basis for any nonequilibrium modeling. In the first paper of this series we established how, by a…
The automated construction of coarse-grained models represents a pivotal component in computer simulation of physical systems and is a key enabler in various analysis and design tasks related to uncertainty quantification. Pertinent methods…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
As an important set of thermodynamic quantities, knowledge of the equation of state over a broad range of temperatures and chemical potentials in the QCD phase diagram is crucial for our understanding of strongly-interacting matter. There…
We investigate how the transport properties of a united atoms fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
An extension of the relativistic density functional approach to the equation of state for strongly interacting matter is suggested which generalizes a recently developed modified excluded-volume mechanism to the case of temperature and…
We consider quasistatic fiber bundle models with interactions. Classical load sharing rules are considered, i.e. local, global or decaying as a power-law of distance. All fibers are identically elastic, initially intact, and break at a…