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Computational Sciences & Mathematics


2014 | 2013

The CM4 team measures its success, in part, on its fundamental contributions to the scientific literature, focusing primarily on mathematics and materials science, as well as the generation and dissemination of algorithms and open-source software.

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Del Razo MJ, W Pan, H Qian, and G Lin. 2014. “Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion.” The Journal of Physical Chemistry B 118(25):7037-7046. DOI: 10.1021/jp5030125.

Deng M and GE Karniadakis. 2014. “Electrostatic correlations near charged planar surfaces.” The Journal of Chemical Physics 141(9):094703. DOI: 10.1063/1.4894053.

Deng M and GE Karniadakis. 2014. “Coarse-Grained Modeling of Protein Unfolding Dynamics.” Multiscale Modeling & Simulation 12(1):109-118. DOI: 10.1137/130921519.

Karagiannis G and G Lin. 2014 “Selection of Polynomial Chaos Bases via Bayesian Model Uncertainty Methods with Applications to Sparse Approximation of PDEs with Stochastic Inputs.” Journal of Computational Physics 259:114-134. DOI: 10.1016/

Kim C and GE Karniadakis. 2014. “Time Correlation Functions of Brownian Motion and Evaluation of Friction Coefficient in the Near-Brownian-Limit Regime.” Multiscale Modeling & Simulation 12(1):225-248. DOI: 10.1137/130929916.

Liang F, Y Cheng, and G Lin. 2014. “Simulated Stochastic Approximation Annealing for Global Optimization with a Square-Root Cooling Schedule.” Journal of the American Statistical Association 109(506):847-863. DOI: 10.1080/01621459.2013.872993.

Li W, G Lin, and D Zhang. 2014. “An adaptive ANOVA-based PCKF for high-dimensional nonlinear inverse modeling.” Journal of Computational Physics 258:752-772. DOI: 10.1016/

Li Z, X Bian, B Caswell, and GE Karniadakis. 2014. “Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwanzig formulation.” Soft Matter, Accepted Manuscript, Published Online September 08, 2014. DOI: 10.1039/C4SM01387E.

Li Z, Y-H Tang, H Lei, B Caswell, and GE Karniadakis. 2014. “Energy-conserving dissipative particle dynamics with temperature-dependent properties.” Journal of Computational Physics 265:113-127. DOI: 10.1016/

Pan W, J Bao, and AM Tartakovsky. 2014. “Smoothed Particle Hydrodynamics Continuous Boundary Force Method for Navier-Stokes Equations Subject to a Robin Boundary Condition.” Journal of Computational Physics 259:242-259. DOI: 10.1016/

Perdikaris P and GE Karniadakis. 2014. “Fractional-order Viscoelasticity in One-dimensional Blood Flow Models.” Annals of Biomedical Engineering 42(5):1012-1023. DOI: 10.1007/s10439-014-0970-3.

Plunkett P, J Hu, C Siefert, and PJ Atzberger. 2014. “Spatially adaptive stochastic methods for fluid-structure interactions subject to thermal fluctuations in domains with complex geometries.” Journal of Computational Physics 277:121-137. DOI: 10.1016/

Quemeneur F, JK Sigurdsson, M Renner, PJ Atzberger, P Bassereau, and D Lacoste. 2014. “Shape matters in protein mobility within membranes.” Proceedings of the National Academy of Sciences of the United States of America 111(14):5083-5087. DOI: 10.1073/pnas.1321054111.

Tang Y-H and GE Karniadakis. 2014. “Accelerating dissipative particle dynamics simulations on GPUs: Algorithms, numerics and applications.” Computer Physics Communications 185(11):2809-2822. DOI: 10.1016/j.cpc.2014.06.015.

Venturi D and GE Karniadakis. 2014. “Convolutionless Nakajima-Zwanzig Equations for Stochastic Analysis in Nonlinear Dynamical Systems.” Proceedings of the Royal Society A 470(2166):20130754. DOI: 10.1098/rspa.2013.0754.

Zayernouri M and GE Karniadakis. 2014. “Exponentially accurate spectral and spectral element methods for fractional ODEs.” Journal of Computational Physics 257(Part A):460-480. DOI: 10.1016/

Zayernouri M and GE Karniadakis. 2014. “Fractional Spectral Collocation Method.” SIAM Journal on Scientific Computing 36(1):A40-A62. DOI: 10.1137/130933216.

Zhang Z, MV Tretyakov, B Rozovskii, and GE Karniadakis. 2014. “A Recursive Sparse Grid Collocation Method for Differential Equations with White Noise.” SIAM Journal on Scientific Computing 36(4):A1652-A1677. DOI: 10.1137/130938906.


Fedosov D, M Dao, GE Karniadakis, and S Suresh. 2013. “Computational Biorheology of Human Blood Flow in Health and Disease.” Annals of Biomedical Engineering, Special Issue: Frontiers in Bioengineering. Published Online, Oct. 12, 2013. DOI: 10.1007/s10439-013-0922-3.

Kim C and GE Karniadakis. 2013. “Microscopic theory of Brownian motion revisited: The Rayleigh Model.” Physical Review E 87(3):032129. DOI: 10.1103/PhysRevE.87.032129.

Lei H and GE Karniadakis. 2013. “Probing vasoocclusion phenomena in sickle cell anemia via mesoscopic simulations.” Proceedings of the National Academy of Sciences (PNAS) 110(28):11326-11330. DOI: 10.1073/pnas.1221297110.

Pan W and AM Tartakovsky. 2013. “Dissipative particle dynamics model for colloid transport in porous media.” Advances in Water Resources 58:41-48. DOI: 10.1016/j.advwatres.2013.04.004.

Peng Z, X Li, I Pivkin, M Dao, GE Karniadakis, and S Suresh. 2013. “Lipid-bilayer and cytoskeletal interactions in a red blood cell.” Proceedings of the National Academy of Sciences (PNAS) 110(33):13356-13361. DOI: 10.1073/pnas.1311827110.

Rolfe BA, J Chun, and YL Joo. 2013. “Dynamics of Micelle-Nanoparticle Systems Undergoing Shear: A Coarse-Grained Molecular Dynamics Approach.” Soft Matter, 9(43):10294-10305. DOI: 10.1039/C3SM52194J.

Stinis P. 2013. “Renormalized reduced models for singular PDEs.” Communications in Applied Mathematics and Computational Science 8(1):39-66. DOI: 10.2140/camcos.2013.8.39.

Wang Y, JK Sigurdsson, E Brandt, and PJ Atzberger. 2013. “Dynamic implicit-solvent coarse-grained models of lipid bilayer membranes: Fluctuating hydrodynamics thermostat.” Physical Review E 88(2):023301. DOI: 10.1103/PhysRevE.88.023301.

Zayernouri M and GE Karniadakis. 2013. “Fractional Sturm-Liouville eigen-problems: Theory and numerical approximation.” Journal of Computational Physics 252(1):495-517. DOI: 10.1016/

Collaboratory on Mathematics for Mesoscopic Modeling of Materials (CM4)


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