This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are discussed at length, and the consequences arising from the loss of detail are given. Finally, a large number of results are presented to give the reader a feeling for the types of problem which can be addressed.

A hydrophilic directional slippery rough surface outperforms conventional liquid-repellent surfaces in water harvesting.

Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion necessary for antimicrobial or synthetic pore formation are poorly understood. We observe a lipid-assisted mechanism for passive insertion into a model membrane from molecular dynamics simulations. The assembly used in the study, a generic nanotube functionalized with hydrophilic termini, is assisted in crossing the membrane core by transleaflet lipid flips. Lipid tails occlude a purely hydrophobic nanotube. The observed insertion mechanism requirements for hydrophobic-hydrophilic matching have implications for the design of synthetic channels and antibiotics.T he interaction between biological membranes and synthetic or natural macromolecules that have activity through the formation of transmembrane nanopores is intrinsic to the functioning of ion channels (1-8) and antimicrobial peptides (6, 9). It is surprising, therefore, that the insertion mechanism of amphiphilic molecules into (and even across) biomembranes is poorly understood (10-13). The use of fully atomistic computer simulations to probe the interactions of membrane proteins with lipid bilayers is of considerable current interest (8). However, despite many recent successes, such simulations are hampered by the accessible system size and timescale. To glean some insight into possible mechanisms associated with the membrane insertion process we have used molecular dynamics (MD) calculations to study the interaction of tubular macromolecules with a fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer in its physiologically relevant liquid-crystalline phase. The calculations we report have been carried out by using a coarse-grain (CG) model, inspired by the model successfully used to study self-organizing surfactant systems (14). The tubular nanostructures we study are generic models for preassembled bundles of membrane-spanning proteins (3, 11), antimicrobial peptides (4), and cyclic peptides (1) and for a synthetic nanosyringe based on functionalizing a carbon nanotube (2, 15). Although many naturally existing ion channels and antimicrobial peptides form pores with a hydrophilic lumen, many systems exist, including viral ion channels, synthetic peptides, and nanodevices, for which the present model should be an adequate description.The present simulations involve molecular systems that represent Ϸ70,000 atoms altogether. Simulations with larger systems have been reported (8,16). The present CG approach, however, allows us to routinely calculate dynamics in the hundreds or thousands of nanoseconds and therefore allows us to study events that take place at longer scales than those currently accessible by all-atom calculations. Methods CG Model. In the CG model (17, 18), each DMPC lipid molecule consists of 13 interaction sites, eight of which are hydrophobic (four for each alkanoyl tail) and five of which are hydrophilic, three for the glycerol moiety ...

An analysis of the structural and dynamical hydrogen bonding interactions at the lipid water interface from a 10 ns molecular dynamics simulation of a hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer is presented. We find that the average number of hydrogen bonds per lipid oxygen atom varies depending on its position within the lipid. Radial distribution functions are reported for water interacting with lipid oxygen, nitrogen, and phosphorus atoms, as well as for lipid-lipid interactions. The extent of inter-and intramolecular lipid-water-lipid hydrogen bond bridges is explored along with charge pair associations among headgroups of different lipid molecules. We also examine the hydrogen bonding dynamics of water at the lipid surface. A picture emerges of a sticky interface where water that is hydrogen bonded to lipid oxygen atoms diffuses slowly. Hydrogen bonds between water and the double bonded lipid oxygen atoms are longer lived than those to single bonded lipid oxygen atoms, and hydrogen bonds between water and the tail lipid oxygen atoms are longer lived than those to headgroup oxygen atoms. The implications of these results for lateral proton transfer at the interface are also discussed.

The statistical mechanics of systems whose evolution is governed by mixed quantum-classical dynamics is investigated. The algebraic properties of the quantum-classical time evolution of operators and of the density matrix are examined and compared to those of full quantum mechanics. The equilibrium density matrix that appears in this formulation is stationary under the dynamics and a method for its calculation is presented. The response of a quantum-classical system to an external force which is applied from the distant past when the system is in equilibrium is determined. The structure of the resulting equilibrium time correlation function is examined and the quantum-classical limits of equivalent quantum time correlation functions are derived. The results provide a framework for the computation of equilibrium time correlation functions for mixed quantum-classical systems. (C) 2001 American Institute of Physics