Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

The hydrophobic effect — the tendency for oil and water to segregate — is important in diverse phenomena, from the cleaning of laundry, to the creation of micro-emulsions to make new materials, to the assembly of proteins into functional complexes. This effect is multifaceted depending on whether hydrophobic molecules are individually hydrated or driven to assemble into larger structures. Despite the basic principles underlying the hydrophobic effect being qualitatively well understood, only recently have theoretical developments begun to explain and quantify many features of this ubiquitous phenomenon.

/pdf/interfaces-and-the-driving-force-of-hydrophobic-assembly-2hgxjxkvur.pdf

Interfaces and the driving force of hydrophobic assembly

The bulk-heterojunction blend of an electron donor and an electron acceptor material is the key component in a solution-processed organic photovoltaic device. In the past decades, a p-type conjugated polymer and an n-type fullerene derivative have been the most commonly used electron donor and electron acceptor, respectively. While most advances of the device performance come from the design of new polymer donors, fullerene derivatives have almost been exclusively used as electron acceptors in organic photovoltaics. Recently, nonfullerene acceptor materials, particularly small molecules and oligomers, have emerged as a promising alternative to replace fullerene derivatives. Compared to fullerenes, these new acceptors are generally synthesized from diversified, low-cost routes based on building block materials with extraordinary chemical, thermal, and photostability. The facile functionalization of these molecules affords excellent tunability to their optoelectronic and electrochemical properties. Within t...

Nonfullerene Acceptor Molecules for Bulk Heterojunction Organic Solar Cells

Dye-sensitized solar cells (DSCs) are attractive because they are made from cheap materials that do not need to be highly purified and can be printed at low cost 1 . DSCs are unique compared with almost all other kinds of solar cells in that electron transport, light absorption and hole transport are each handled by different materials in the cell 2,3 . The sensitizing dye in a DSC is anchored to a wide-bandgap semiconductor such as TiO2, SnO2 or ZnO. When the dye absorbs light, the photoexcited electron rapidly transfers to the conduction band of the semiconductor, which carries the electron to one of the electrodes 4 . A redox couple, usually comprised of iodide/triiodide (I – /I3 – ), then reduces the oxidized dye back to its neutral state and transports the positive charge to the platinized counter-electrode 5 . In 1991, O’Regan and Gratzel demonstrated that a film of titania (TiO2) nanoparticles deposited on a DSC would act as a mesoporous n-type photoanode and thereby increase the available surface area for dye attachment by a factor of more than a thousand 1 . This approach dramatically improved light absorption and brought power-conversion efficiencies into a range that allowed the DSC to be viewed as a serious competitor to other solar cell technologies 6 . A schematic and energy level diagram showing the operation of a typical DSC is shown in Fig. 1. During the 1990s and the early 2000s, researchers found that organometallic complexes based on ruthenium provided the highest power-conversion efficiencies 7,8

/pdf/the-renaissance-of-dye-sensitized-solar-cells-3i1cludwp0.pdf

The renaissance of dye-sensitized solar cells

Using molecular dynamics simulations of an atomistic water model, we study the interfacial hydrodynamic slippage of water at various hydrophobic surfaces, both organic (silane monolayers) and inorganic (diamondlike and Lennard-Jones models). The measured slip lengths range from nanometers to tens of nanometers. Slip lengths on different surfaces are found to collapse nearly onto a single curve as a function of the static contact angle characterizing the surface wettability, thereby suggesting a quasiuniversal relationship. This dependence is rationalized on the basis of a simple scaling description of the fluid-solid friction at the microscopic level. The link between slippage and water depletion at hydrophobic surfaces is clarified. These results shed light on the controversy over experimental measurements of the slip length at smooth hydrophobic surfaces.

/pdf/water-slippage-versus-contact-angle-a-quasiuniversal-2ewgku129i.pdf

Water slippage versus contact angle: a quasiuniversal relationship.

The Lum–Chandler–Weeks theory of hydrophobicity [Lum, K., Chandler, D. & Weeks, J. D. (1999) J. Phys. Chem. 103, 4570–4577] is applied to treat the temperature dependence of hydrophobic solvation in water. The application illustrates how the temperature dependence for hydrophobic surfaces extending less than 1 nm differs significantly from that for surfaces extending more than 1 nm. The latter is the result of water depletion, a collective effect, that appears at length scales of 1 nm and larger. Because of the contrasting behaviors at small and large length scales, hydrophobicity by itself can explain the variable behavior of entropies of protein folding.

https://www.pnas.org/content/pnas/97/15/8324.full.pdf

Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding

We have studied the effect of weak solute−solvent attractions on the solvation of nonpolar molecules in water at ambient conditions using an extension and improved parameterization of the theory of solvation due to Lum, Chandler, and Weeks [J. Phys. Chem. B 1999, 103, 4570]. With a reasonable strength of alkane−water interactions, an accurate prediction of the alkane−water interfacial tension is obtained. As previously established for solutes with no attractive interactions with water, the free energy of solvation scales with volume for small solutes and with surface area for large solutes. The crossover to the latter regime occurs on a molecular length scale. It is associated with the formation of a liquid−vaporlike interface, a drying interface, between the large hydrophobic solute and liquid water. In the absence of attractions, this interface typically lies more than one solvent molecular diameter away from the hard sphere surface. With the addition of attractive interactions between water and the har...

/pdf/the-hydrophobic-effect-and-the-influence-of-solute-solvent-3ucsk72ui7.pdf

The hydrophobic effect and the influence of solute-solvent attractions

Encapsulation of biomacromolecules in metal–organic frameworks (MOFs) can preserve biological functionality in harsh environments. Despite the success of this approach, termed biomimietic mineralization, limited consideration has been given to the chemistry of the MOF coating. Here, we show that enzymes encapsulated within hydrophilic MAF-7 or ZIF-90 retain enzymatic activity upon encapsulation and when exposed to high temperatures, denaturing or proteolytic agents, and organic solvents, whereas hydrophobic ZIF-8 affords inactive catalase and negligible protection to urease.

Enhanced Activity of Enzymes Encapsulated in Hydrophilic Metal-Organic Frameworks.

We have calculated the free energy of solvation for hard sphere solutes, as large as 20 A in diameter, in two simple-point-charge models of water. These results were obtained using umbrella sampling of ensembles with fixed, ambient temperature and pressure. For the same water models, we have also calculated the surface tension of a liquid−vapor interface at room temperature. Analogous calculations were carried out for three thermodynamic states of the Lennard-Jones (LJ) fluid near liquid−vapor coexistence. For both water and the LJ fluid at the conditions we have simulated, extrapolation of our results suggests that the planar interface between coexisting liquid and vapor phases has the same surface tension as the planar limit of hard sphere solvation. We expect this correspondence to be a general result for fluids at thermodynamic states close to phase coexistence, as measured by the difference in chemical potential between bulk liquid and vapor phases, and far from the critical point. The solvation free...

/pdf/scaling-of-hydrophobic-solvation-free-energies-1bcml81p36.pdf

David M. Huang

Papers

Water slippage versus contact angle: a quasiuniversal relationship.

Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding

The hydrophobic effect and the influence of solute-solvent attractions

Enhanced Activity of Enzymes Encapsulated in Hydrophilic Metal-Organic Frameworks.

Scaling of Hydrophobic Solvation Free Energies