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Items: 1 to 50 of 114

1.

Density-dependent finite system-size effects in equilibrium molecular dynamics estimation of shear viscosity: Hydrodynamic and configurational study.

Kim KS, Kim C, Karniadakis GE, Lee EK, Kozak JJ.

J Chem Phys. 2019 Sep 14;151(10):104101. doi: 10.1063/1.5113751.

PMID:
31521071
2.

Quantitative prediction of erythrocyte sickling for the development of advanced sickle cell therapies.

Lu L, Li Z, Li H, Li X, Vekilov PG, Karniadakis GE.

Sci Adv. 2019 Aug 21;5(8):eaax3905. doi: 10.1126/sciadv.aax3905. eCollection 2019 Aug.

3.

Linking Gaussian process regression with data-driven manifold embeddings for nonlinear data fusion.

Lee S, Dietrich F, Karniadakis GE, Kevrekidis IG.

Interface Focus. 2019 Jun 6;9(3):20180083. doi: 10.1098/rsfs.2018.0083. Epub 2019 Apr 19.

PMID:
31065346
4.

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces.

Wang Y, Li Z, Xu J, Yang C, Karniadakis GE.

Soft Matter. 2019 Feb 20;15(8):1747-1757. doi: 10.1039/c8sm02170h.

PMID:
30672954
5.

Self-Cleaning of Hydrophobic Rough Surfaces by Coalescence-Induced Wetting Transition.

Zhang K, Li Z, Maxey M, Chen S, Karniadakis GE.

Langmuir. 2019 Feb 12;35(6):2431-2442. doi: 10.1021/acs.langmuir.8b03664. Epub 2019 Jan 25.

PMID:
30640480
6.

Quantifying Shear-Induced Deformation and Detachment of Individual Adherent Sickle Red Blood Cells.

Deng Y, Papageorgiou DP, Chang HY, Abidi SZ, Li X, Dao M, Karniadakis GE.

Biophys J. 2019 Jan 22;116(2):360-371. doi: 10.1016/j.bpj.2018.12.008. Epub 2018 Dec 18.

PMID:
30612714
7.

Quantifying Platelet Margination in Diabetic Blood Flow.

Chang HY, Yazdani A, Li X, Douglas KAA, Mantzoros CS, Karniadakis GE.

Biophys J. 2018 Oct 2;115(7):1371-1382. doi: 10.1016/j.bpj.2018.08.031. Epub 2018 Aug 30.

8.

Mechanics of diseased red blood cells in human spleen and consequences for hereditary blood disorders.

Li H, Lu L, Li X, Buffet PA, Dao M, Karniadakis GE, Suresh S.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9574-9579. doi: 10.1073/pnas.1806501115. Epub 2018 Sep 6.

9.

Simultaneous polymerization and adhesion under hypoxia in sickle cell disease.

Papageorgiou DP, Abidi SZ, Chang HY, Li X, Kato GJ, Karniadakis GE, Suresh S, Dao M.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9473-9478. doi: 10.1073/pnas.1807405115. Epub 2018 Sep 6.

10.

Understanding the Twisted Structure of Amyloid Fibrils via Molecular Simulations.

Lu L, Deng Y, Li X, Li H, Karniadakis GE.

J Phys Chem B. 2018 Dec 13;122(49):11302-11310. doi: 10.1021/acs.jpcb.8b07255. Epub 2018 Aug 27.

PMID:
30106299
11.

Omics, big data and machine learning as tools to propel understanding of biological mechanisms and to discover novel diagnostics and therapeutics.

Perakakis N, Yazdani A, Karniadakis GE, Mantzoros C.

Metabolism. 2018 Oct;87:A1-A9. doi: 10.1016/j.metabol.2018.08.002. Epub 2018 Aug 8. No abstract available.

12.

Nature of intrinsic uncertainties in equilibrium molecular dynamics estimation of shear viscosity for simple and complex fluids.

Kim KS, Han MH, Kim C, Li Z, Karniadakis GE, Lee EK.

J Chem Phys. 2018 Jul 28;149(4):044510. doi: 10.1063/1.5035119.

PMID:
30068169
13.

Cytoskeleton Remodeling Induces Membrane Stiffness and Stability Changes of Maturing Reticulocytes.

Li H, Yang J, Chu TT, Naidu R, Lu L, Chandramohanadas R, Dao M, Karniadakis GE.

Biophys J. 2018 Apr 24;114(8):2014-2023. doi: 10.1016/j.bpj.2018.03.004.

14.

Data-driven Modeling of Hemodynamics and its Role on Thrombus Size and Shape in Aortic Dissections.

Yazdani A, Li H, Bersi MR, Di Achille P, Insley J, Humphrey JD, Karniadakis GE.

Sci Rep. 2018 Feb 6;8(1):2515. doi: 10.1038/s41598-018-20603-x.

15.

Publisher's Note: "Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion" [J. Chem. Phys. 147, 244110 (2017)].

Yoshimoto Y, Li Z, Kinefuchi I, Karniadakis GE.

J Chem Phys. 2018 Jan 28;148(4):049901. doi: 10.1063/1.5023012. No abstract available.

PMID:
29390814
16.

An atomistic fingerprint algorithm for learning ab initio molecular force fields.

Tang YH, Zhang D, Karniadakis GE.

J Chem Phys. 2018 Jan 21;148(3):034101. doi: 10.1063/1.5008630.

PMID:
29352799
17.

Molecular hydrodynamics: Vortex formation and sound wave propagation.

Han KH, Kim C, Talkner P, Karniadakis GE, Lee EK.

J Chem Phys. 2018 Jan 14;148(2):024506. doi: 10.1063/1.5011992.

18.

Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion.

Yoshimoto Y, Li Z, Kinefuchi I, Karniadakis GE.

J Chem Phys. 2017 Dec 28;147(24):244110. doi: 10.1063/1.5009041. Erratum in: J Chem Phys. 2018 Jan 28;148(4):049901.

PMID:
29289151
19.

Fractional modeling of viscoelasticity in 3D cerebral arteries and aneurysms.

Yu Y, Perdikaris P, Karniadakis GE.

J Comput Phys. 2016 Oct 15;323:219-242. doi: 10.1016/j.jcp.2016.06.038. Epub 2016 Jul 11.

20.

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

Blumers AL, Tang YH, Li Z, Li X, Karniadakis GE.

Comput Phys Commun. 2017 Aug;217:171-179. doi: 10.1016/j.cpc.2017.03.016. Epub 2017 Apr 18.

21.

A deep convolutional neural network for classification of red blood cells in sickle cell anemia.

Xu M, Papageorgiou DP, Abidi SZ, Dao M, Zhao H, Karniadakis GE.

PLoS Comput Biol. 2017 Oct 19;13(10):e1005746. doi: 10.1371/journal.pcbi.1005746. eCollection 2017 Oct.

22.

Modeling of Biomechanics and Biorheology of Red Blood Cells in Type 2 Diabetes Mellitus.

Chang HY, Li X, Karniadakis GE.

Biophys J. 2017 Jul 25;113(2):481-490. doi: 10.1016/j.bpj.2017.06.015.

23.

Mesoscopic Adaptive Resolution Scheme toward Understanding of Interactions between Sickle Cell Fibers.

Lu L, Li H, Bian X, Li X, Karniadakis GE.

Biophys J. 2017 Jul 11;113(1):48-59. doi: 10.1016/j.bpj.2017.05.050.

24.

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution.

Tang YH, Lu L, Li H, Evangelinos C, Grinberg L, Sachdeva V, Karniadakis GE.

Biophys J. 2017 May 23;112(10):2030-2037. doi: 10.1016/j.bpj.2017.04.020.

25.

Nonlinear information fusion algorithms for data-efficient multi-fidelity modelling.

Perdikaris P, Raissi M, Damianou A, Lawrence ND, Karniadakis GE.

Proc Math Phys Eng Sci. 2017 Feb;473(2198):20160751. doi: 10.1098/rspa.2016.0751.

26.

Patient-specific modeling of individual sickle cell behavior under transient hypoxia.

Li X, Du E, Dao M, Suresh S, Karniadakis GE.

PLoS Comput Biol. 2017 Mar 13;13(3):e1005426. doi: 10.1371/journal.pcbi.1005426. eCollection 2017 Mar.

27.

A General Shear-Dependent Model for Thrombus Formation.

Yazdani A, Li H, Humphrey JD, Karniadakis GE.

PLoS Comput Biol. 2017 Jan 17;13(1):e1005291. doi: 10.1371/journal.pcbi.1005291. eCollection 2017 Jan.

28.

Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts.

Li Z, Lee HS, Darve E, Karniadakis GE.

J Chem Phys. 2017 Jan 7;146(1):014104. doi: 10.1063/1.4973347.

PMID:
28063444
29.

Biomechanics and biorheology of red blood cells in sickle cell anemia.

Li X, Dao M, Lykotrafitis G, Karniadakis GE.

J Biomech. 2017 Jan 4;50:34-41. doi: 10.1016/j.jbiomech.2016.11.022. Epub 2016 Nov 12. Review.

30.

MD/DPD Multiscale Framework for Predicting Morphology and Stresses of Red Blood Cells in Health and Disease.

Chang HY, Li X, Li H, Karniadakis GE.

PLoS Comput Biol. 2016 Oct 28;12(10):e1005173. doi: 10.1371/journal.pcbi.1005173. eCollection 2016 Oct.

31.

cDPD: A new dissipative particle dynamics method for modeling electrokinetic phenomena at the mesoscale.

Deng M, Li Z, Borodin O, Karniadakis GE.

J Chem Phys. 2016 Oct 14;145(14):144109.

PMID:
27782504
32.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach.

Rausch MK, Karniadakis GE, Humphrey JD.

Biomech Model Mechanobiol. 2017 Feb;16(1):249-261. doi: 10.1007/s10237-016-0814-1. Epub 2016 Aug 18.

33.

A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization.

Li Z, Bian X, Yang X, Karniadakis GE.

J Chem Phys. 2016 Jul 28;145(4):044102. doi: 10.1063/1.4959121.

PMID:
27475343
34.

111 years of Brownian motion.

Bian X, Kim C, Karniadakis GE.

Soft Matter. 2016 Aug 14;12(30):6331-46. doi: 10.1039/c6sm01153e. Epub 2016 Jul 11.

35.

Visualizing multiphysics, fluid-structure interaction phenomena in intracranial aneurysms.

Perdikaris P, Insley JA, Grinberg L, Yu Y, Papka ME, Karniadakis GE.

Parallel Comput. 2016 Jul;55:9-16. doi: 10.1016/j.parco.2015.10.016. Epub 2015 Dec 15.

36.

Biomechanics of red blood cells in human spleen and consequences for physiology and disease.

Pivkin IV, Peng Z, Karniadakis GE, Buffet PA, Dao M, Suresh S.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):7804-9. doi: 10.1073/pnas.1606751113. Epub 2016 Jun 27. Erratum in: Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4521.

37.

Model inversion via multi-fidelity Bayesian optimization: a new paradigm for parameter estimation in haemodynamics, and beyond.

Perdikaris P, Karniadakis GE.

J R Soc Interface. 2016 May;13(118). pii: 20151107. doi: 10.1098/rsif.2015.1107.

38.

Probing the Twisted Structure of Sickle Hemoglobin Fibers via Particle Simulations.

Lu L, Li X, Vekilov PG, Karniadakis GE.

Biophys J. 2016 May 10;110(9):2085-93. doi: 10.1016/j.bpj.2016.04.002.

39.

Sub-cellular modeling of platelet transport in blood flow through microchannels with constriction.

Yazdani A, Karniadakis GE.

Soft Matter. 2016 May 11;12(19):4339-51. doi: 10.1039/c6sm00154h.

40.

Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow.

Bian X, Deng M, Tang YH, Karniadakis GE.

Phys Rev E. 2016 Mar;93(3):033312. doi: 10.1103/PhysRevE.93.033312. Epub 2016 Mar 28.

PMID:
27078489
41.

Multiscale modeling and simulation of brain blood flow.

Perdikaris P, Grinberg L, Karniadakis GE.

Phys Fluids (1994). 2016 Feb;28(2):021304. Epub 2016 Feb 8.

42.

Patient-specific blood rheology in sickle-cell anaemia.

Li X, Du E, Lei H, Tang YH, Dao M, Suresh S, Karniadakis GE.

Interface Focus. 2016 Feb 6;6(1):20150065. doi: 10.1098/rsfs.2015.0065.

43.

A discrete mesoscopic particle model of the mechanics of a multi-constituent arterial wall.

Witthoft A, Yazdani A, Peng Z, Bellini C, Humphrey JD, Karniadakis GE.

J R Soc Interface. 2016 Jan;13(114):20150964. doi: 10.1098/rsif.2015.0964.

44.

Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.

Li Z, Bian X, Li X, Karniadakis GE.

J Chem Phys. 2015 Dec 28;143(24):243128. doi: 10.1063/1.4935490.

45.

Fluctuating hydrodynamics in periodic domains and heterogeneous adjacent multidomains: Thermal equilibrium.

Bian X, Li Z, Deng M, Karniadakis GE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Nov;92(5):053302. doi: 10.1103/PhysRevE.92.053302. Epub 2015 Nov 10.

PMID:
26651811
46.

Multi-fidelity modelling via recursive co-kriging and Gaussian-Markov random fields.

Perdikaris P, Venturi D, Royset JO, Karniadakis GE.

Proc Math Phys Eng Sci. 2015 Jul 8;471(2179):20150018.

47.

Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees.

Lykov K, Li X, Lei H, Pivkin IV, Karniadakis GE.

PLoS Comput Biol. 2015 Aug 28;11(8):e1004410. doi: 10.1371/journal.pcbi.1004410. eCollection 2015 Aug.

48.

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems.

Li Z, Yazdani A, Tartakovsky A, Karniadakis GE.

J Chem Phys. 2015 Jul 7;143(1):014101. doi: 10.1063/1.4923254.

49.

Mesoscale modeling of phase transition dynamics of thermoresponsive polymers.

Li Z, Tang YH, Li X, Karniadakis GE.

Chem Commun (Camb). 2015 Jul 14;51(55):11038-40. doi: 10.1039/c5cc01684c.

PMID:
26062446
50.

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow.

Deng M, Grinberg L, Caswell B, Karniadakis GE.

Soft Matter. 2015 Jun 28;11(24):4962-72. doi: 10.1039/c4sm02395a.

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