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

http://www.ced.berkeley.edu/downloads/research/LUP.parks.pdf

Urban green space, public health, and environmental justice: The challenge of making cities ‘just green enough’

In recent years, zwitterionic materials such as poly(carboxybetaine) (pCB) and poly(sulfobetaine) (pSB) have been applied to a broad range of biomedical and engineering materials. Due to electrostatically induced hydration, surfaces coated with zwitterionic groups are highly resistant to nonspecific protein adsorption, bacterial adhesion, and biofilm formation. Among zwitterionic materials, pCB is unique due to its abundant functional groups for the convenient immobilization of biomolecules. pCB can also be prepared in a hydrolyzable form as cationic pCB esters, which can kill bacteria or condense DNA. The hydrolysis of cationic pCB esters into nonfouling zwitterionic groups will lead to the release of killed microbes or the irreversible unpackaging of DNA. Furthermore, mixed-charge materials have been shown to be equivalent to zwitterionic materials in resisting nonspecific protein adsorption when they are uniformly mixed at the molecular scale.

Ultralow-Fouling, Functionalizable, and Hydrolyzable Zwitterionic Materials and Their Derivatives for Biological Applications

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

http://ideaexchange.uakron.edu/cgi/viewcontent.cgi?article=1230&context=chemengin_ideas

Surface Hydration: Principles and Applications Toward Low-fouling/nonfouling Biomaterials

Molecular simulations were performed to study the interactions between a protein (lysozyme, LYZ) and phosphorylcholine-terminated self-assembled monolayers (PC-SAMs) in the presence of explicit water molecules and ions. The results show that the water molecules above the PC-SAM surface create a strong repulsive force on the protein as it approaches the surface. The structural and dynamic properties of the water molecules above the PC-SAM surface were analyzed to provide information regarding the role of hydration in surface resistance to protein adsorption. It can be seen from residence time dynamics that the water molecules immediately above the PC-SAM surface are significantly slowed down as compared to bulk water, suggesting that the PC-SAM surface generates a tightly bound, structured water layer around its head groups. Moreover, the orientational distribution and reorientational dynamics of the interfacial water molecules near the PC-SAM surface were found to have the ionic solvation nature of the PC...

Molecular simulation studies of protein interactions with zwitterionic phosphorylcholine self-assembled monolayers in the presence of water.

Resistance of mixed self-assembled monolayers (SAMs) with various counter-charged terminal groups of different valence and protonation/deprotonation states to nonspecific protein adsorption is investigated. It is demonstrated that excellent nonfouling surfaces can be readily constructed from mixed positively and negatively charged components of equal valence in a wide range of thiol solution compositions. Furthermore, the lattice structure of one of the mixed SAM systems studied is revealed by atomic force microscopy (AFM) to be (5.2 ± 0.2 A × 5.2 ± 0.2 A)60°. Results indicate that the packing structure of mixed charged SAMs is determined by strong charge−charge interactions of the terminal groups rather than S−Au and chain−chain interactions. This work provides direct evidence that conformational flexibility is not required for protein resistance of a surface and even a single compact layer of charged groups of balanced charge with a crystalline structure can resist nonspecific protein adsorption, sugges...

Strong resistance of a thin crystalline layer of balanced charged groups to protein adsorption.

In this work, we report a study on the differential hydration of carboxybetaine and sulfobetaine using molecular simulations. The coordination number, spatial distribution, dipole orientation distribution, and residence time of water molecules around the positively charged group (N(CH3)3+) and negatively charged group (COO− for carboxybetaine and SO3− for sulfobetaine) were investigated to compare the hydration of these two betaines. The results show that the negatively charged group of sulfobetaine has more water molecules around it than that of carboxybetaine, while the water molecules around the negatively charged group of the carboxybetaine have a sharper spatial distribution, more preferential dipole orientation, and longer residence time. The behavior of water molecules around the positively charged group of sulfobetaine is similar to those around the positively charged group of carboxybetaine. For both sulfobetaine and carboxybetaine, the positively charged groups are surrounded by more water molec...

Difference in hydration between carboxybetaine and sulfobetaine.

MIL-101(Cr) has drawn much attention due to its high stability compared with other metal-organic frameworks. In this study, three trace flue gas contaminants (H2O, NO, SO2) were each added to a 10 vol% CO2/N2 feed flow and found to have a minimal impact on the adsorption capacity of CO2. In dynamic CO2 regeneration experiments, complete regeneration occurred in 10 min at 328 K for temperature swing adsorption-N2-stripping under a 50 cm(3)/min N2 flow and at 348 K for vacuum-temperature swing adsorption at 20 KPa. Almost 99% of the pre-regeneration adsorption capacity was preserved after 5 cycles of adsorption/desorption under a gas flow of 10 vol% CO2, 100 ppm SO2, 100 ppm NO, and 10% RH, respectively. Strong resistance to flue gas contaminants, mild recovery conditions, and excellent recycling efficiency make MIL-101(Cr) an attractive adsorbent support for CO2 capture.

/pdf/adsorption-of-carbon-dioxide-by-mil-101-cr-regeneration-5buw4slzib.pdf

Adsorption of Carbon Dioxide by MIL-101(Cr): Regeneration Conditions and Influence of Flue Gas Contaminants

A rechargeable Li metal anode coupled with a high-voltage cathode is a promising approach to high-energy-density batteries exceeding 300  Wh kg-1 . Reported here is an advanced dual-additive electrolyte containing a unique solvation structure and it comprises a tris(pentafluorophenyl)borane additive and LiNO3 in a carbonate-based electrolyte. This system generates a robust outer Li2 O solid electrolyte interface and F- and B-containing conformal cathode electrolyte interphase. The resulting stable ion transport kinetics enables excellent cycling of Li/LiNi0.8 Mn0.1 Co0.1 O2 for 140 cycles with 80 % capacity retention under highly challenging conditions (≈295.1 Wh kg-1 at cell-level). The electrolyte also exhibits high cycling stability for a 4.6 V LiCoO2 (160 cycles with 89.8 % capacity retention) cathode and 4.95 V LiNi0.5 Mn1.5 O4 cathode.

Yi He

Papers

Molecular simulation studies of protein interactions with zwitterionic phosphorylcholine self-assembled monolayers in the presence of water.

Strong resistance of a thin crystalline layer of balanced charged groups to protein adsorption.

Difference in hydration between carboxybetaine and sulfobetaine.

Adsorption of Carbon Dioxide by MIL-101(Cr): Regeneration Conditions and Influence of Flue Gas Contaminants

Synergistic Dual‐Additive Electrolyte Enables Practical Lithium‐Metal Batteries