Atomistic vs. Coarse Grained Simulations all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative.

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Presentation transcript:

Atomistic vs. Coarse Grained Simulations all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative slow (ns) vs. fast (ms) 1 coarse grained water 4 atomistic water  atomistic coarse grained

composition: 1600 DPPC H2O 15 ns50 ns100 ns 180 ns250 ns150 ns 1 ns 5 ns0 ns cell size: 20x20x20 nm simulation time: 250 ns Aggregation into a DPPC bilayer – coarse grained model

starting structure (t=0 ns) Surrounding water Aggregation of DPPC into vesicles composition: 1600 DPPC H2O cell size: 30x30x30 nm simulation time: 100 ns

0 ns random5 ns worms 10 ns bicelle 60 ns cup 20 ns bicelle 80 ns vesicle

LAMELLAR STALK HEMIFUSION FUSION PORE RHOMBIC CUBIC HEXAGONAL

Lamellar to Hexagonal Transition for DOPE at low hydration in agreement with experiment (Rand etal) t = 0ns t = 20 ns t = 100 ns T=280 -> 320K stalk formation hexagonal phase

t = 20 ns t = 100 ns stalk formation hexagonal phase

Folding Transition States in Proteins In collaboration with the group of Chris Dobson in Cambridge we have looked at transition states in the folding of SH3 domains. Objective: To evaluate the folding propensity of proposed transition states (TS) of the a-spectrin SH3 domain using molecular dynamics (MD) simulations with an explicit representation of the solvent. Some of the proposed transition states fold other do not.

Init Native run 1 Configuration 3 Configuration 4 run 2 Configuration 2 Examples showing the native state, a proposed transition state and results of 2 independent folding simulations. Folding successful Folding unsuccessful

Status of our contribution: 1.Trajectories of the simulations mentioned above can be made available on request 2.While we have not appointed anyone specifically on the project we are in the process of advertising. 3.Our aim is to specifically appoint a person focusing on code development who could interact with those groups involved in methods development and exploit our preexisting simulations..