Simulating complex fluids or in general complex molecular systems requires approaches covering decades of time and length scales. This usually cannot be achieved within one simulation model. Over the years many different methods and models have been developed ranging from rather generic models, representing most efficiently the universal statistical mechanical properties of e.g. polymers, to all atom models and even quantum mechanical treatments. While these allow for scientifically very important studies in their own right, only a combination and close link between models of different levels allows for a truly quantitative description of materials and processes. In the present contribution we discuss an adaptive resolution approach where different levels of detail are treated within one simulation and the molecules are free to diffuse between different regions in space, where the molecules interact with different interaction potentials.
COBISS.SI-ID: 4764186
Simulation schemes for liquids or strongly fluctuating systems that allow to change the molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surroundings introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures a thermodynamic equilibrium among molecules of different representations. The robustness of the algorithm is tested for two examples, namely, an adaptive resolution simulation, atomistic/coarse grained, for a liquid of tetrahedral molecules, and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.
COBISS.SI-ID: 4379162
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.
COBISS.SI-ID: 4728090
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. Our multiscale approach is designed for molecular simulations of open domains with relatively large molecules, either in the grand canonical ensemble or under non-equilibrium conditions.
COBISS.SI-ID: 4329754
We show that the MD simulation with fluctuating number of degrees of freedom is feasible only with the application of a thermostat.
COBISS.SI-ID: 4760602