The Burnett Problem: Molecular Dynamics' Grand Challenge
نویسنده
چکیده
The nonlinear Burnett coeecients are the Tay-lor series coeecients for the functional dependence describing how the Thermodynamic Flux responds to a Thermodynamic Force acting on a uid. Ernst et. al. computed the functional dependence exactly for a hard disk/sphere uid (a uid made up of idealised billiard balls) undergoing shear ow, and found that the relationship was non-analytic, i.e. that the nonlinear Burnett coeecients were innnite. It is of considerable interest to know if these coeecients are nite for other uids, particularly uids of industrial importance. Theoretical work by this author and collaborators allow the possibility of a Molecular Dynamics calculation of the Bur-nett coeecients. For some years, the Burnett project has been working to perform this calculation for a Lennard-Jones Fluid with 108 particles. The current incarnation of this project couples the 128 processor CM5 located at Adelaide University, the 1024 processor AP1000 located at Fujitsu Parallel Laboratory, the 20 processor Power Challenge located at the Parallel Computing and Visualisation Laboratory, Redfern, Sydney and an 12 processor Convex SPP2000 located at UNSW to form a sustained aggregate computing facility of 11.5GFlops. 1 The Burnett Problem Molecular Dynamics Simulations refer to simulating a uid by solving the equations of motion for its substituent particles (the molecules). Typical simulations have only a few hundred molecules, but some simulations have been done involving hundreds of thousands. Even though only a microscopic chunk of the uid is simulated , many bulk properties of the system can be obtained from it. More detailed theoretical and practical information can be found in Refss5, 1]. The bulk properties are related to Transient Time Correlation Functions, which typically have the form hA(?(0))B(?(t))i, where ?(t) refers to the positions and momenta of all the molecules at time t, and hi implies that this quantity has been averaged over an ensemble of systems and/or over time. Nonlinear transport coeecients (or nonlinear Burnett coeecientss2]), B i , give a Taylor series representation of a nonlinear transport coee-cient L, in terms of the thermodynamic force F, i.e. if a thermodynamic ux J is written in terms of the coeecient's deening constitutive relation as J = L(F)F, then the Burnett coeecients are related example, in the case of electrical conductivity, we may write the relation between the current density j and the electric eld E as j = (E)E. In this case, (0) is the usual Ohmic conductivity. The Burnett coeecients have …
منابع مشابه
Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...
متن کاملPrediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling
Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structures to model the backbone flexibility and molecular dynamics simulations to model the sidechain and ligand flexibility. The methods are tested for t...
متن کاملScalability of a tera-scale linux-based clusters for parallel ab initio molecular dynamics applications
KISTI supercomputing center has initiated a TeraCluster project to build a linux-based cluster with tera-flops performance. The main goal of the project is to provide a resources composed of PC clusters that meet the level of computing power required by the grand challenge applications in Korea. In the beginning of 2002, we have built a prototype of TeraCluster with 128 computing nodes, Phase-I...
متن کاملModern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org/ ). The challenge was focused on the ligands of the farnesoid X receptor (FXR), a highly flexible nuclear receptor of the cholesterol derivative c...
متن کاملMultiplexed-replica exchange molecular dynamics method for protein folding simulation.
Simulating protein folding thermodynamics starting purely from a protein sequence is a grand challenge of computational biology. Here, we present an algorithm to calculate a canonical distribution from molecular dynamics simulation of protein folding. This algorithm is based on the replica exchange method where the kinetic trapping problem is overcome by exchanging noninteracting replicas simul...
متن کامل