Scalable parallel molecular dynamics algorithms for organic systems

A scalable parallel algorithm, Macro-Molecular Dynamics (MMD), has been developed for large-scale molecular dynamics simulations of organic macromolecules, based on space-time multi-resolution techniques and dynamic management of distributed lists. The algorithm also includes the calculation of long range forces using Fast Multipole Method (FMM). FMM is based on the octree data structure, in which each parent cell is divided into 8 child cells and this division continues until the cell size is equal to the non-bonded interaction cutoff length. Due to constant number of operations performed at each stage of the octree, the FMM algorithm scales as O(N). Design and analysis of MMD and FMM algorithms are presented. Scalability tests are performed on three tera-flop machines: 1024-processor Intel Xeon-based Linux cluster, SuperMike at LSU, 1184-processor IBM SP4 Marcellus and the 512-processor Compaq AlphaServer Emerald at the U.S. Army Engineer Research and Development Center (ERDC) MSRC. The tests show that the Linux cluster outperforms the SP4 for the MMD application. The tests also show significant effects of memory- and cache-sharing on the performance

Molecular-dynamics simulations of self-assembled monolayers (SAM) on parallel computers

The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25o along next-nearest neighbor direction at 300K. At 350K the system transforms to a disordered phase characterized by small tilt angle, flexible tilt direction, and random distribution of backbone planes. With increasing lattice spacing, a, the tilt angle increases rapidly from a nearly zero value at a = 4.7Å to as high as 34 o at a = 5.3Å at 300K. We also studied the effect of end groups on the tilt structure of SAM films. We characterized the system with respect to temperature, the alkane chain length, lattice spacing, and the length of the end group. We found that the gauche defects were predominant only in the tails, and the gauche defects increased with the temperature and number of EG units. Effect of electric field on the structure of poly (ethylene glycol) (PEG) terminated alkanethiol self assembled monolayer (SAM) on gold has been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied anti-parallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside

Atomistic simulations of a multicomponent asymmetric lipid bilayer

The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid bilayer system comprising of an unsaturated POPC (palmitoyl-oleoyl-phosphatidyl-choline), a saturated SM (sphingomyelin) and cholesterol are investigated. In these simulations, the initial stages of liquid ordered, $l_o$, domain formation are observed and such domains are found to be highly enriched in cholesterol and SM. The current simulations also suggest that the cholesterol molecules may partition into these SM-dominated regions in the ratio of $3:1$ when compared to POPC-dominated regions. SM molecules exhibit a measurable tilt and long range tilt correlations are observed within the $l_o$ domain as a consequence of the asymmetry of the bilayer, with implications to local membrane deformation and budding. Tagged particle diffusion for SM and cholesterol molecules, which reflects spatial variations in the physical environment encountered by the tagged particle, is computed and compared with recent experimental results obtained from high resolution microscopy.Comment: Manuscript with 5 figures, Supplementary Information, 10 Supplementary Figure

The conformational phase diagram of neutral polymers in the presence of attractive crowders

Extensive coarse grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowded densities, the polymer predominantly shows three phases as a function of both intra polymer and polymer-crowder interactions: (1) weak intra polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E) (2) strong intra polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI) and (3) strong polymer-crowder attractive interactions, regardless of intra polymer interactions, induce a second collapsed or globular conformation that encloses bridging crowders (phase CB). The detailed phase diagram is obtained by determining the phase boundaries delineating the different phases based on an analysis of the radius of gyration as well as bridging crowders. The dependence of the phase diagram on strength of crowder-crowder attractive interactions and crowder density is clarified. We also show that when the crowder density is increased, a third collapsed phase of the polymer emerges for weak intra polymer attractive interactions. This crowder density induced compaction is shown to be enhanced by stronger crowder-crowder attraction and is different from the depletion induced collapse mechanism which is primarily driven by repulsive interactions. We also provide a unified explanation of the observed reentrant swollen/extended conformations of earlier simulations of weak and strongly self interacting polymers in terms of crowder-crowder attractive interactions

Onset of glassiness in two-dimensional ring polymers: interplay of stiffness and crowding

The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is observed with increasing pressure and thereby a phase space for equilibrium dynamics is identified in the plane of obtained monomer density and ring stiffness. When the rings are highly flexible, i.e. low ring stiffness, glassiness sets in via crowding of crumpled polymers which take a globular form. In contrast, at large ring stiffness, when the rings tend to have large asphericity under compaction, we observe the emergence of local domains having orientational ordering, at high pressures. Thus, our simulations highlight how varying the deformability of rings leads to contrasting mechanisms in driving the system towards the glassy regime.Comment: Supplementary Information added as ancillary documen