1. what are the limitations in MD simulations? Name What are the advantages of using periodic boundary condition for MD?

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1 1. what are the limitations in MD simulations? Name What are the advantages of using periodic boundary condition for MD? Name 2

2 3. what is the metropolis Monte Carlo simulation?

3 4. Why argon is chosen for the simulation of correlation in the liquid state?

4 5. How does NPT algorithm (constant pressure) work?

5 6. why do we need molecular dynamics simulations for the dislocations?

6 7. what determines the size of grain for the simulation (see figure). Name 2.

7 8. what is an application of polymer-nanotube MD simulations?

8 9. What are the limitations of molecular dynamics simulations for protein folding? Name 2

9 10. What determines the size of the micelle in MD simulations? 11. why do we need molecular dynamics simulations in addition to experiments for micelles?

10 12. what are the applications of coarse grained simulations?

11 Width (nm) 13. What are the challenges in linking simulation and experiments? Timescale >min s s a O(300 nm, s) O(Å, ns) Nonreactive MD Micropipette Nanoindentation Mesoscale models Continuum models MEMS testing Collagen fibril Optical/ magnetic tweezers Atomic force microscopy c b 10 ns ps QM/ DFT Reactive MD Tomography Transmission elctron microscopy (e.g. cryo) LIF 450 nm 500 nm 280 nm 5 0 Å DNA polypeptides X-ray diffraction NMR nm Secondary protein structures (e.g. -sheets, -helices) Nanoparticles (nanowires, carbon nanotubes) m Cells m Tissues organs organisms Length scale

12 14. What is hydrogen bonding? (See figure below) 15. Why water is difficult to simulate? Name 2

13 news & views the twentieth century. e work of Pierre-Gilles de Gennes was key in shaping the strategies in contemporary LC research. e aims of this research are shi ing away 16. What is the molecular mechanics is useful for? from the quest for better gures of merit in electro-optical applications towards the search for smart functional materials. Interdisciplinary links to biological and biotechnological systems, colloids and elastomer sciences have emerged; all were re ected at the meeting. Fascinating progress has been achieved in the eld of LC colloidal systems, in particular nematic colloids; nematic LC phases consist of (usually) rod-like molecules that have directional, but no positional, ordering. Locally, the director eld designates the preferred orientation. Nematic colloids are formed by small inclusions, such as droplets, spheres or rods in the host phase. e self-organized alignment of water droplets in a nematic colloid was rst shown by Poulin et al. 2 ; since then this eld has grown rapidly and re ned considerably. e elastic forces of the nematic host + + Figure 1 Entangled colloidal particles in a nematic LC. The top image shows the equilibrium structure of six 4.5- m microspheres bound by a disclination loop. In the central image, two laser traps (red crosses) are used to stretch the chain. The bottom image is a computer simulation; the red line marks the low-order-parameter region around the disclination. The images are courtesy of Igor Muševič. in wh and p comp Sh the th of th in an medi Univ bacte bacte stran sectio know form Livol be us trans phag leavin Cryo studi of th in th comp chira

14 17. what is self assembly? 18. what are the applications of self-assembly of soft shells?

15 ecule into a and C), the ecule in its erved. This ion that an nal (disenaged) state. very rapid hen the die would be image in its d that the nd the sixwhich allity. s to make rotational barrier of 117 kj/mol was obtained. Here, the central HB-DC forms a ratchet in the cavity and, hence, has no significant rotational degree of freedom at room temperature. In the disengaged state, the rotor is first shifted 0.26 nm out of registry with the molecular lattice (Fig. 3). This is sufficient to the t-butyl groups in contact was observed to reorient. In addition, we calculated a translation-energy what barrier are to move the HB-DC applications from ground (white) of noise supramolecular (17). It has nevertheless cause work cannot be extracted from back- 20. the engaged to the disengaged position of bearings? 42 kj/mol. ThisName consistent with 2 our observation of a low rate of lateral shuttle action driven by kt as observed in Fig. 3 when the The potential energy profile shown in Fig. 4C is highly asymmetric, but periodic in the engaged state. Chemically driven protein motors (15) and unimolecular ratchets (16) also have asymmetric rotational potentials. These potentials are reminiscent of Feynman s ratchet and pawl devised to show that it is lower its rotation barrier to 29 kj/mol, and the not possible to extract unidirectional rotation- 19. Why copper is selected for the substrate for central HB-DC is now free to rotate. This is in excellent agreement with our observations. STM As HB-DC measurements? was rotated, the conformation of al work from the background thermal noise (17). Similar to Maxwell s demon (18), the second law of thermodynamics cannot be violated by such macroscopic devices, be- been proposed that work can be extracted, using an asymmetric periodic potential, if a secondary colored noise is applied and therefore rectified by the system (14). In the spirit on April 3, 2012 Downloaded from Fig. 4. Model of the molecular mechanics