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Articles

Mesoscale biosimulations within a unified framework: from proteins to plasmids

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Pages 101-112 | Received 29 Dec 2017, Accepted 12 Dec 2018, Published online: 09 Jan 2019

References

  • Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nature Struct Bio. 2002;9:646–652. doi: 10.1038/nsb0902-646
  • Makarov V, Pettitt BM, Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res. 2002;35:376–384. doi: 10.1021/ar0100273
  • Levitt M. The birth of computational structural biology. Nat Struct Mol Biol. 2001;8:392. doi: 10.1038/87545
  • McCammon JA, Karplus M. The dynamic picture of protein structure. Acc Chem Res. 1983;16:187–193. doi: 10.1021/ar00090a001
  • Ponder JW, Case DA. Force fields for protein simulations. Adv Protein Chem. 2003;66:27. doi: 10.1016/S0065-3233(03)66002-X
  • Karplus M, Levitt M, Warshel A. Nobel Prize in Chemistry 2013. Nobel Media AB. 2013;Oct 9:2014.
  • Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4:187. doi: 10.1002/jcc.540040211
  • Abraham MJ, Murtola T, Schulz R, et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1:19–25. doi: 10.1016/j.softx.2015.06.001
  • Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1995;117:5179–5197. doi: 10.1021/ja00124a002
  • Salomon-Ferrer R, Case DA, Walker RC. An overview of the Amber biomolecular simulation package. Wiley Interdisciplinary Rev. 2013;3:198.
  • Smith W, Yong C, Rodger P. DL_POLY: application to molecular simulation. Mol Simul. 2002;28:385–471. doi: 10.1080/08927020290018769
  • James C P, Wang RBW, Gumbart J, et al. Scalable molecular dynamics with NAMD. J Comp Chem. 2005;26:1781–1802. doi: 10.1002/jcc.20289
  • Anderson JA, Lorenz CD, Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units. J Comput Phys. 2008;227:5342. doi: 10.1016/j.jcp.2008.01.047
  • Shaw DE, Maragakis P, Lindorff-Larsen K, et al. Atomic-level characterization of the structural dynamics of proteins. Science. 2010;330:341. doi: 10.1126/science.1187409
  • Shaw DE, Deneroff MM, Dror RO. Anton, a special-purpose machine for molecular dynamics simulation. Commun ACM. 2008;51:91. doi: 10.1145/1364782.1364802
  • Kamerlin SC, Vicatos S, Dryga A. Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu Rev Phys Chem. 2011;62:41. doi:10.1146/annurev-physchem-032210-103335
  • Lyubartsev AP, Laaksonen A. Calculation of effective interaction potentials from radial distribution functions: a reverse monte carlo approach. Phys Rev E. 1995;52:3730–3737. doi: 10.1103/PhysRevE.52.3730
  • Reith D, Pütz M, Müller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem. 2003;24:1624. doi: 10.1002/jcc.10307
  • de Jong DH, Singh G, Bennett WFD, et al. Improved parameters for the Martini Coarse-Grained protein force field. J Chem Theory Comput. 2013;9:687–697. doi: 10.1021/ct300646g
  • Bellesia G, Shea J-E. Effect of-sheet propensity on peptide aggregation. J Chem Phys. 2009;130:145103. doi: 10.1063/1.3108461
  • Davtyan A, Schafer NP, Zheng W, et al. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure Biasing. J Phys Chem B. 2012;116:8494–8503. doi: 10.1021/jp212541y
  • Kar P, Gopal SM, Cheng Y-M, et al. PRIMO: a transferable Coarse-Grained force field for proteins. J Chem Theory Comput. 2013;9:3769–3788. doi: 10.1021/ct400230y
  • Maisuradze G, Senet P, Czaplewski C, Investigation of protein folding by Coarse-Grained molecular dynamics with the UNRES force field. J Phys Chem B. 2010;114:4471–4485. doi: 10.1021/jp9117776
  • Sterpone F, Melchionna S, Tuffery P, et al. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev. 2014;43:4871–4893. doi: 10.1039/C4CS00048J
  • Ermak DL, McCammon JA. Brownian dynamics with hydrodynamic interactions. J Chem Phys. 1978;69:1352–1360. doi: 10.1063/1.436761
  • Schmidt RR, Cifre JGH, de la Torre JG. Comparison of Brownian dynamics algorithms with hydrodynamic interaction. J Chem Phys. 2011;135:084116. doi: 10.1063/1.3626868
  • Zgorski A, Lyman E. Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini. Biophys J. 2016;111:2689. doi: 10.1016/j.bpj.2016.11.010
  • Ando T, Skolnick J. On the importance of hydrodynamic interactions in lipid membrane formation. Biophys J. 2013;104:96–105. doi: 10.1016/j.bpj.2012.11.3829
  • Arnarez C, Uusitalo JJ, Masman MF, et al. Dry Martini, a Coarse-Grained force field for lipid membrane simulations with implicit solvent. J Chem Theory Comput. 2014;11:260–275. doi: 10.1021/ct500477k
  • Succi S. The lattice Boltzmann equation: for fluid dynamics and beyond. Oxford: Oxford University Press; 2001.
  • Bernaschi M, Melchionna S, Succi S. MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations. Comput Phys Commun. 2009;180:1495. doi: 10.1016/j.cpc.2009.04.001
  • Yeomans J. Mesoscale simulations: lattice Boltzmann and particle algorithms. Phys A. 2006;369:159–184. doi: 10.1016/j.physa.2006.04.011
  • Ahlrichs P, Dünweg B. Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics. J Chem Phys. 1999;111:8225. doi: 10.1063/1.480156
  • Dünweg B, Ladd AJ. Lattice Boltzmann simulations of soft matter systems. In: Advanced computer simulation approaches for soft matter sciences III. Springer; 2009. p. 89–166.
  • Forester T, Smith W. Dlpoly, ccp5 program library; 2001.
  • Phillips JC, Braun R, Wang W. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781. doi: 10.1002/jcc.20289
  • Chebaro Y, Pasquali S, Derreumaux P. The Coarse-Grained OPEP force field for non-amyloid and amyloid proteins. J Phys Chem B. 2012;116:8741–8752. doi: 10.1021/jp301665f
  • Groot RD, Warren PB. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J Chem Phys. 1997;107:4423. doi: 10.1063/1.474784
  • Cercignani C, Berman A. Theory and application of the Boltzmann equation. J Appl Mech. 1976;43:521. doi: 10.1115/1.3423913
  • Bhatnagar PL, Gross EP, Krook M. A model for collision processes in Gases. I. small amplitude processes in charged and neutral one-component systems. Phys Rev. 1954;94:511–525. doi: 10.1103/PhysRev.94.511
  • Succi S. The lattice Boltmzann equation for fluid dynamics and beyond. Oxford: Clarendon Press; 2001.
  • Higuera F, Succi S, Benzi R. Lattice gas dynamics with enhanced collisions. EPL (Europhysics Letters). 1989;9:345–349. doi: 10.1209/0295-5075/9/4/008
  • Benzi R, Succi S, Vergassola M. The lattice Boltzmann equation: theory and applications. Phys Rep. 1992;222:145–197. doi: 10.1016/0370-1573(92)90090-M
  • Guo Z, Zhen C, Shi B. Discrete lattice effects on the forcing term in the lattice Boltzmann method. Phys Rev E. 2002;65:046308.
  • Datar AV, Fyta M, Marconi UMB, et al. Electro kinetic Lattice Boltzmann solver coupled to molecular dynamics: application to polymertranslocation. Langmuir. 2017;33(42):11635–11645. doi: 10.1021/acs.langmuir.7b01997
  • Marconi UMB, Melchionna S. Kinetic theory of correlated fluids: from dynamic density functional to Lattice Boltzmann methods. J Chem Phys. 2009;131:014105. doi: 10.1063/1.3166865
  • Landau LD, Lifshitz EM. Fluid mechanics. London: Pergamon Press; 1963.
  • Ladd AJ. Short-time motion of colloidal particles: numerical simulation via a fluctuating lattice-Boltzmann equation. Phys Rev Lett. 1993;70:1339–1342. doi: 10.1103/PhysRevLett.70.1339
  • Dünweg B, Schiller UD, Ladd AJ. Statistical mechanics of the fluctuating lattice Boltzmann equation. Phys Rev E. 2007;76:036704. doi: 10.1103/PhysRevE.76.036704
  • Adhikari R, Stratford K, Cates M, et al. Fluctuating lattice Boltzmann. EPL (Europhysics Letters). 2005;71:473–479. doi: 10.1209/epl/i2004-10542-5
  • Peskin CS. The immersed boundary method. Acta numerica. 2002;11:479. doi: 10.1017/S0962492902000077
  • Nash R, Adhikari R, Cates M. Singular forces and pointlike colloids in lattice Boltzmann hydrodynamics. Phys Rev E. 2008;77:026709. doi: 10.1103/PhysRevE.77.026709
  • Schiller UD. A unified operator splitting approach for multi-scale fluid-particle coupling in the lattice Boltzmann method. Comput Phys Commun. 2014;185:2586. doi: 10.1016/j.cpc.2014.06.005
  • Kalthoff W, Schwarzer S, Ristow G, et al. On the application of a novel algorithm to hydrodynamic diffusion and velocity fluctuations in sedimenting systems. Int J Modern Phys C. 1996;7:543–561. doi: 10.1142/S0129183196000466
  • Ahlrichs P, Dünweg B. Lattice-Boltzmann simulation of polymer-solvent systems. Int J Modern Phys C. 1998;9:1429–1438. doi: 10.1142/S0129183198001291
  • Melchionna S. Design of quasisymplectic propagators for Langevin dynamics. J Chem Phys. 2007;127:044108. doi: 10.1063/1.2753496
  • Chikatamarla S, Ansumali S, Karlin I. Entropic lattice Boltzmann models for hydrodynamics in three dimensions. Phys Rev Lett. 2006;97:010201.
  • http://www.palabos.org/.
  • Limbach H-J, Arnold A, Mann BA. ESPResSo—an extensible simulation package for research on soft matter systems. Comput Phys Commun. 2006;174:704. doi: 10.1016/j.cpc.2005.10.005
  • Gray A, Hart A, Henrich O, et al. Scaling soft matter physics to thousands of graphics processing units in parallel. Int J High Perform Comput Appl. 2015;29:274–283. doi: 10.1177/1094342015576848
  • Seaton MA, Anderson RL, Metz S, et al. DL_MESO: highly scalable mesoscale simulations. Mol Simul. 2013;39:796–821. doi: 10.1080/08927022.2013.772297
  • Schmieschek S, Shamardin L, Frijters S. LB3D: A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids. Comput Phys Commun. 2017;217:149. doi: 10.1016/j.cpc.2017.03.013
  • Sterpone F, Derreumaux P, Melchionna S. Protein simulations in fluids: coupling the OPEP Coarse-Grained force field with hydrodynamics. J Chem Theory Comput. 2015;11:1843–1853. doi: 10.1021/ct501015h
  • Chiricotto M, Melchionna S, Derreumaux P. Hydrodynamic effects on-amyloid (16–22) peptide aggregation. J Chem Phys. 2016;145(3):035102. doi: 10.1063/1.4958323
  • Chiricotto M, Sterpone F, Derreumaux P, et al. Multiscale simulation of molecular processes in cellular environments. Philos Trans A Math Phys Eng Sci. 2016;374(2080):pii: 20160225. doi: 10.1098/rsta.2016.0225
  • Sterpone F, Doutreligne S, Tran TT. Multi-scale simulations of biological systems using the OPEP coarse-grained model. Bioch Biophys Res Comm. 2017;498(2):296–304. doi: 10.1016/j.bbrc.2017.08.165
  • Bernaschi M, Bisson M, Fatica M, et al. In Proceedings of the international conference on high performance computing, networking, storage and analysis, ACM; 2013. p. 2.
  • Roosen-Runge F, Hennig M, Zhang F, et al. Protein self-diffusion in crowded solutions. Proc Natl Acad Sci USA. 2011;108:11815–11820. doi: 10.1073/pnas.1107287108
  • Wang Y, Li C, Pielak GJ. Effects of proteins on protein diffusion. J Am Chem Soc. 2010;132:9392–9397. doi: 10.1021/ja102296k
  • Nasica-Labouze J, Nguyen PH, Sterpone F, et al. Amyloid protein and Alzheimers disease: when computer simulations complement experimental studies. Chem Rev. 2015;115:3518–3563. doi: 10.1021/cr500638n
  • Senn HM, Thiel W. QM/MM methods for biomolecular systems. Angewandte Chemie Int Edition. 2009;48:1198–1229. doi: 10.1002/anie.200802019
  • Praprotnik M, Site LD, Kremer K. Multiscale simulation of soft matter: from scale bridging to adaptive resolution. Annu Rev Phys Chem. 2008;59:545–571. doi: 10.1146/annurev.physchem.59.032607.093707
  • Springer TA. von Willebrand factor, Jedi knight of the bloodstream. Blood. 2014;124:1412–1425. doi: 10.1182/blood-2014-05-378638
  • Fyta MG, Melchionna S, Kaxiras E, et al. Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore. Multiscale Model Simul. 2006;5:1156–1173. doi: 10.1137/060660576
  • Fyta M, Melchionna S, Succi S, et al. Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: Theory and multiscale simulations. Phys Rev E. 2008;78:036704. doi: 10.1103/PhysRevE.78.036704
  • Fyta M, Melchionna S, Succi S. Translocation of biomolecules through solid-state nanopores: Theory meets experiments. J Polymer Sci Part B. 2011;49:985–1011. doi: 10.1002/polb.22284
  • Ouldridge TE, Louis AA, Doye JP. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys. 2011;134:02B627. doi: 10.1063/1.3552946
  • Hsu CW, Fyta M, Lakatos G. Ab initio determination of coarse-grained interactions in double-stranded DNA. J Chem Phys. 2012;137:105102. doi: 10.1063/1.4748105
  • Morão AM, Nunes JC, Sousa F. Ultrafiltration of supercoiled plasmid DNA: modeling and application. J Memb Sci. 2011;378:280. doi: 10.1016/j.memsci.2011.05.017
  • Gompper G, Ihle T, Kroll D. Multi-particle collision dynamics: a particle-based mesoscale simulation approach to the hydrodynamics of complex fluids. In: Holm C, Kremer K, editors. Advanced computer simulation approaches for soft matter sciences III. Advances in polymer science Vol. 221. Berlin: Springer; 2009. p. 1–87.
  • Shaw DE. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem. 2005;26:1318. doi: 10.1002/jcc.20267
  • Bowers KJ, Dror RO, Shaw DE. The midpoint method for parallelization of particle simulations. J Chem Phys. 2006;124. doi: 10.1063/1.2191489

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