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.

Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.

The Chemistry and Applications of Metal-Organic Frameworks

Adsorptive separation is very important in industry. Generally, the process uses porous solid materials such as zeolites, activated carbons, or silica gels as adsorbents. With an ever increasing need for a more efficient, energy-saving, and environmentally benign procedure for gas separation, adsorbents with tailored structures and tunable surface properties must be found. Metal–organic frameworks (MOFs), constructed by metal-containing nodes connected by organic bridges, are such a new type of porous materials. They are promising candidates as adsorbents for gas separations due to their large surface areas, adjustable pore sizes and controllable properties, as well as acceptable thermal stability. This critical review starts with a brief introduction to gas separation and purification based on selective adsorption, followed by a review of gas selective adsorption in rigid and flexible MOFs. Based on possible mechanisms, selective adsorptions observed in MOFs are classified, and primary relationships between adsorption properties and framework features are analyzed. As a specific example of tailor-made MOFs, mesh-adjustable molecular sieves are emphasized and the underlying working mechanism elucidated. In addition to the experimental aspect, theoretical investigations from adsorption equilibrium to diffusion dynamics via molecular simulations are also briefly reviewed. Furthermore, gas separations in MOFs, including the molecular sieving effect, kinetic separation, the quantum sieving effect for H2/D2 separation, and MOF-based membranes are also summarized (227 references).

Selective gas adsorption and separation in metal–organic frameworks

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

https://www.pnas.org/content/pnas/99/20/12562.full.pdf

Escaping free-energy minima

Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymers

The thermal transitions of confined polymers are important for the application of polymers in molecular scale devices and advanced nanotechnology. However, thermal transitions of ultrathin polymer assemblies confined in subnanometre spaces are poorly understood. In this study, we show that incorporation of polyethylene glycol (PEG) into nanochannels of porous coordination polymers (PCPs) enabled observation of thermal transitions of the chain assemblies by differential scanning calorimetry. The pore size and surface functionality of PCPs can be tailored to study the transition behaviour of confined polymers. The transition temperature of PEG in PCPs was determined by manipulating the pore size and the pore-polymer interactions. It is also striking that the transition temperature of the confined PEG decreased as the molecular weight of PEG increased.

/pdf/unveiling-thermal-transitions-of-polymers-in-subnanometre-3v5z4roufc.pdf

Unveiling thermal transitions of polymers in subnanometre pores

For a slow open quantum subsystem weakly coupled to a fast thermal bath, we derive the general form of the slippage to be applied to the initial conditions of the Redfield master equation. This slippage is given by a superoperator which describes the non-Markovian dynamics of the subsystem during the short-time relaxation of the thermal bath. We verify in an example that the Redfield equation preserves positivity after the slippage superoperator has been applied to the initial density matrix of the subsystem. For δ-correlated baths, the Redfield master equation reduces to the Lindblad master equation and the slippage of initial conditions vanishes consistently.

Slippage of initial conditions for the Redfield master equation

Molecules confined in nanospaces will have distinctly different properties to those in the bulk state because of the formation of specific molecular assemblies and conformations. We studied the chain conformation and dynamics of single polystyrene (PSt) chains confined in highly regular one-dimensional nanochannels of a porous coordination polymer [Zn2(bdc)2ted]n (1; bdc = 1,4-benzenedicarboxylate, ted = triethylenediamine). Characterization by two-dimensional (2D) heteronuclear 1H−13C NMR gave a direct demonstration of the nanocomposite formation and the intimacy between the PSt and the pore surfaces of 1. Calorimetric analysis of the composite did not reveal any glass transition of PSt, which illustrates the different nature of the PSt encapsulated in the nanochannels compared with that of bulk PSt. From N2 adsorption measurements, the apparent density of PSt in the nanochannel was estimated to be 0.55 g cm−3, which is much lower than that of bulk PSt. Results of a solid-state 2H NMR study of the compos...

Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace

The performance increase of the lithium-ion battery (LIB) is critical for effectively leveling the cyclic nature of renewable energy sources related to the global warming. The current LIB performance with liquid electrolytes, e.g., ethylene carbonate (EC) and propylene carbonate (PC), is strongly dependent on a stable solid electrolyte interphase (SEI) films on the electrode surfaces. However, such electrolyte-dependent SEI film formation still remains not-fully understood. To investigate its microscopic characteristics, we have performed the atomistic reaction simulations with the recently developed hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method, and have exposed for the first time the atomistic picture of the structure of the SEI films consistent with the experimental evidence and conjectures. It was also found that the dense EC-based SEI film can protect electrolyte from the reduction, providing the cavities which have sufficient size for passing of Li+ cations. In contrast, the PC-bas...

On Electrolyte-Dependent Formation of Solid Electrolyte Interphase Film in Lithium-Ion Batteries: Strong Sensitivity to Small Structural Difference of Electrolyte Molecules

Masataka Nagaoka

Papers

Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymers

Unveiling thermal transitions of polymers in subnanometre pores

Slippage of initial conditions for the Redfield master equation

Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace

On Electrolyte-Dependent Formation of Solid Electrolyte Interphase Film in Lithium-Ion Batteries: Strong Sensitivity to Small Structural Difference of Electrolyte Molecules