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

Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.

Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer

The structure of molecular systems dictates the physical properties, and symmetry is the determining factor for all electronic properties. This makes group theory a powerful tool in quantum mechanics to compute molecular properties. For inorganic compounds, the coordination geometry has been estimated as idealized polyhedra with high symmetry, which, through ligand field theory, provides predictive capabilities. However, real samples rarely have ideal symmetry, and although continuous shape measures (CShM) can be used to evaluate deviation from an ideal reference structure σideal, this often fails for lanthanide(III) complexes with high coordination numbers, no obvious choice of principal axes, and no obvious reference structure. In lanthanide complexes, the unique electronic structures and associated properties are intricately tied to the symmetry around the lanthanide center. Therefore, robust methodologies to evaluate and estimate point group symmetry are instrumental for building structure–property relationships. Here, we have demonstrated an algorithmic approach that orients a molecular structure Q in the best possible way to the symmetry axis of any given point group G and computes a deviation from the ideal symmetry σsym(G,Q). This approach does not compute the deviation from an ideal reference system, but the intrinsic deviation in the structure induced by symmetry operations. If the structure contains the symmetry operation, there is no deviation and σsym(G,Q) = 0. The σsym deviation is generated from all of the symmetry operation ÔS in a point group G using the most correct orientation of the sample structure in each group G. The best orientation is found by an algorithm that minimizes the orientation of the structure with respect to G. To demonstrate the methodology, we have investigated the structure and symmetry of 8- and 9-coordinated lanthanide(III) aqua complexes and correlated the luminescence from 3 europium(III) crystals to their actual symmetry. To document the methodology, the approach has been tested on 26 molecules with different symmetries. It was concluded that the method is robust and fully autonomous. 

Evaluation of Point Group Symmetry in Lanthanide(III) Complexes: A New Implementation of a Continuous Symmetry Operation Measure with Autonomous Assignment of the Principal Axis

The structure of molecular systems dictates the physical properties, and symmetry is determining for all electronic properties. This makes group theory a powerful tool in quantum mechanics, when computing molecular properties. For inorganic compounds, the coordination geometry has been estimated as idealized polyhedra of high symmetry, which through ligand field theory provides predictive capabilities. However, real samples rarely have ideal symmetry, and even though continuous symmetry measures can be used to evaluate deviation form ideal symmetry, this often fails for lanthanide(III) complexes with high coordination numbers and no obvious principal axis. In lanthanide complexes, the unique electronic structures and the associated properties are intricately tied to the symmetry around the lanthanide center. Robust methodologies to evaluate and estimate point group symmetry is therefore instrumental for building structure property relationships. Here, we have demonstrated an algorithmic approach that determines the principal axis, and computes a deviation from ideal symmetry. This approach is based on the continuous symmetry measures and evaluates deviations from ideal symmetry for each symmetry operation in all relevant point groups. To demonstrate the methodology we have investigated the structure and symmetry of 8 and 9 coordinated lanthanide(III) aqua complexes, and correlated the luminescence from 3 europium(III) crystals to their actual symmetry. To document the methodology the approach has been tested on 26 molecules with different symmetry. It was concluded that the method is robust and fully autonomous. 

Evaluation of Point Group Symmetry in Lanthanide(III) Complexes – a New Implementation of the Continuous Symmetry Measure with Autonomous Assignment of the Principal Axis

Despite the desirability of polymers for use in many products due to their flexibility, light weight, and durability, their status as thermal insulators has precluded their use in applications where thermal conductors are required. However, recent results suggest that the thermal conductance of polymers can be enhanced and that their heat transport behaviors may be highly sensitive to nanoscale control. Here we use non-equilibrium molecular dynamics (MD) simulations to study the effect of mechanical twist on the steady-state thermal conductance across multi-stranded polyethylene wires. We find that a highly twisted double-helical polyethylene wire can display a thermal conductance up to three times that of its untwisted form, an effect which can be attributed to a structural transition in the strands of the double helix. We also find that in thicker wires composed of many parallel strands, adding just one twist can increase its thermal conductance by over 30%. However, we find that unlike stretching a polymer wire, which causes a monotonic increase in thermal conductance, the effect of twist is highly non-monotonic, and certain amounts of twist can actually decrease the thermal conductance. Finally, we apply the Continuous Chirality Measure (CCM) in an attempt to explore the correlation between heat conductance and chirality. The CCM is found to correlate with twist as expected, but we attribute the observed heat transport behaviors to structural factors other than chirality.

pdf/heat-transport-with-a-twist-3abavfcgvl.pdf

Heat Transport with a Twist

Despite its undeniable problems from a philosophical point of view, the concept of molecular structure, with attributes such as shape and symmetry, directly borrowed from the description of macroscopic objects, is nowadays central to most of the chemical sciences. Descriptions such as "the tetrahedral carbon atom" or "octahedral coordination complexes" are widely used as much in elementary textbooks as in the most up-to-date research articles. The definition of molecular shape is, however, not as simple as it might seem at first sight. Molecules don't behave as macroscopic objects do, and the arrangement of atoms within a molecule changes continuously due to the incessant motion of its constituent particles, nuclei, and electrons. How are molecular shape and symmetry affected by this thermal motion? In this Minireview, we introduce the language of continuous symmetry measures as a new tool to quantitatively describe the effects of temperature on molecular shape and symmetry, enriching in this way the set of molecular descriptors that might be used in the establishment of new empirical structure-property relations, of great interest in concomitant areas such as medicinal chemistry or materials science.

Effects of Temperature on the Shape and Symmetry of Molecules and Solids.

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Effects of Temperature on the Shape and Symmetry of Molecules and Solids.