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Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
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…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
Although the behavior of entangled polymers in startup shear flows with constant shear rates has been thoroughly investigated, the response under creep has not been frequently considered. In this study, primitive chain network simulations,…
Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against…
We present a method that exploits self-consistent simulation of coarse-grained and fine-grained models, in order to analyse properties of physical systems. The method uses the coarse-grained model to obtain a first estimate of the quantity…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
We employ the state-of-the-art molecular dynamics simulations to study the kinetics of phase separation and aging phenomena of segregating binary fluid mixtures imbibed in porous materials. Different random porous structures are considered…
We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability…
A coarse-grained model of dense hard sphere colloids building on simple notions of particle mobility and spatial coherence is presented and shown to reproduce results of experiments and simulations for key quantities such as the…
The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-Polybutadiene melts where each…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
The Kremer-Grest (KG) bead-spring model is a near standard in Molecular Dynamic simulations of generic polymer properties. It owes its popularity to its computational efficiency, rather than its ability to represent specific polymer species…
Coarse-grained simulations of conjugated polymers have become a popular way of investigating the device physics of organic photovoltaics. While UV-Vis spectroscopy remains one of key experimental methods for the interrogation of these…
We investigate, using numerical simulations and analytical arguments, a simple one dimensional model for the swelling or the collapse of a closed polymer chain of size N, representing the dynamical evolution of a polymer in a \Theta-solvent…
We consider the thermal breakage of a tethered polymer chain of discrete segments coupled by Morse potentials under constant tensile stress. The chain dynamics at the onset of fracture is studied analytically by Kramers-Langer…
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)…