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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Responsive polymer materials can adapt to surrounding environments, regulate transport of ions and molecules, change wettability and adhesion of different species on external stimuli, or convert chemical and biochemical signals into optical, electrical, thermal and mechanical signals, and vice versa. These materials are playing an increasingly important part in a diverse range of applications, such as drug delivery, diagnostics, tissue engineering and 'smart' optical systems, as well as biosensors, microelectromechanical systems, coatings and textiles. We review recent advances and challenges in the developments towards applications of stimuli-responsive polymeric materials that are self-assembled from nanostructured building blocks. We also provide a critical outline of emerging developments.

Emerging applications of stimuli-responsive polymer materials

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

/pdf/the-martini-force-field-coarse-grained-model-for-3l11ncr3fg.pdf

The MARTINI force field : Coarse grained model for biomolecular simulations

Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyris...

The MARTINI Coarse-Grained Force Field: Extension to Proteins

The relation between atomistic chemical structure, molecular archi- tecture, molecular weight, and material properties is of basic concern in modern soft material science and includes standard properties of bulk materials and surface and interface aspects, as well as the relation between structure and function in nanoscopic objects and molecular assemblies of both synthetic and biological origin. This all implies a thorough understanding on many length and correspondingly time scales, ranging from (sub)atomistic to macroscopic. Presently, com- puter simulations play an increasingly important, if not central, role. Some problems do not require specific atomistic details, whereas others require them only locally. However, in many cases this strict separation is not sufficient for a comprehensive understanding of systems, and flexible simulation schemes are required that link the different levels of resolution. We here give a general view of the problem regarding soft matter and discuss some specific examples of linked simulation techniques at different resolution levels. We then discuss a recently developed flexible simulation scheme, the AdResS method, which allows one to adaptively change the resolution in certain regions of space on demand.

https://www.researchgate.net/profile/Luigi_Delle_Site/publication/5785059_Multiscale_Simulation_of_Soft_Matter_From_Scale_Bridging_to_Adaptive_Resolution/links/0fcfd5134e36be4806000000.pdf

Multiscale simulation of soft matter: from scale bridging to adaptive resolution.

We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule’s atomic and coarse-grained levels of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, and the other containing only one-particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The hybrid and the atomistically resolved systems have the same stat...

Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

Vibrational spectroscopy studies show that the bulk water bending band becomes narrower with increasing temperature (Marechal, Y. J. Mol. Struct. 1994, 322, 105). Since this counterintuitive effect is not associated with the quantum nature of nuclear motion a molecular dynamics (MD) simulation is expected to reproduce it even in the classical limit. We have performed a classical MD simulation of the flexible simple point charge (SPC) and extended SPC (SPC/E) water models to determine the temperature dependence of the bulk water vibrational spectrum. The intramolecular water potential proposed by Toukan and Rahman, including a stretch−bend coupling term, was applied. We performed MD simulations at −4 and 80 °C to compare the calculated vibrational spectra, in particular, the band associated with the bending mode, with the experiment. The experimentally determined narrowing of the bending band with increasing temperature is not reproducible by MD simulation with the applied force field. However, the results...

/pdf/temperature-dependence-of-water-vibrational-spectrum-a-35hktmos2j.pdf

Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study

We introduce a variation of the dissipative particle dynamics (DPD) thermostat that allows for controlling transport properties of molecular fluids. The standard DPD thermostat acts only on a relative velocity along the interatomic axis. Our extension includes the damping of the perpendicular components of the relative velocity, whilst keeping the advantages of conserving Galilei invariance and within our error bar also hydrodynamics. This leads to a second friction parameter for tuning the transport properties of the system. Numerical simulations of a simple Lennard-Jones fluid and liquid water demonstrate a very sensitive behaviour of the transport properties, e.g., viscosity, on the strength of the new friction parameter. We envisage that the new thermostat will be very useful for the coarse-grained and adaptive resolution simulations of soft matter, where the diffusion constants and viscosities of the coarse-grained models are typically too high/low, respectively, compared to all-atom simulations.

/pdf/transport-properties-controlled-by-a-thermostat-an-extended-2rg52yeiae.pdf

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

The adaptive resolution scheme (AdResS) for efficient hybrid particle-based atomistic/mesoscale molecular dynamics (MD) simulations recently introduced by us, [J. Chem. Phys. 123, 224106 (2005)] is extended to high density molecular liquids with spherical boundaries between the atomistic and mesoscale regions. The key feature of this approach is that it allows for a dynamical change of the number of molecular degrees of freedom during the course of a MD simulation by an on-the-fly switching between the atomistic and mesoscopic levels of detail. Pressure and density variations occurring at the atomistic/mesoscale boundary in the original version are considerably reduced employing the improved methodology presented here.

Matej Praprotnik

Papers

Multiscale simulation of soft matter: from scale bridging to adaptive resolution.

Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids.