Computational Hybrid Soft Materials Laboratory

A perspective on coarse-graining methodologies for biomolecules: resolving self-assembly over extended spatiotemporal scales A. Banerjee, M. Hooten, N. Srouji, R. Welch, J. Shovlin and M. Dutt, Frontiers in Soft Matter (2024), 4:1361066 [Paper]

A coarse-grained Molecular Dynamics study of phase behavior in Co-assembled lipomimetic oligopeptides S. Mushnoori, C. Lu, K. Schmidt, M. Dutt Journal of Molecular Graphics and Modelling (2023), 125, 108624 [Paper]

Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides M. Hooten, A. Banerjee, M. Dutt, Journal of Chemical Theory and Computation (2023) [Paper] [Data] [Code]

A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly A. Banerjee and M. Dutt, The Journal of Chemical Physics (2023), 158, 114105 [Paper] [Data] [Code]

Self-Organization of Mobile, Polyelectrolytic Dendrons on Stable, Amphiphile-Based Spherical Surfaces. A. Banerjee and M. Dutt, Langmuir (2023), 39 (9), 3439–3449 [Paper] [Data] [Code]

Pipelines for automating compliance-based elimination and extension (PACE2): a systematic framework for high-throughput biomolecular materials simulation workflows S. Mushnoori, E. Zang, A. Banerjee, M. Hooten, A. Merzky, M. Turilli, S. Jha, M. Dutt, Journal of Physics: Materials (2023) [Paper] [Code]

Controlling morphology in hybrid isotropic/patchy particle assemblies. S. Mushnoori, J. A. Logan, A.V. Tkachenko and M. Dutt, The Journal of Chemical Physics (2022), 156, 024501. [Paper] [Code]

Symmetry-specific orientational order parameters for complex structures. J. A. Logan, S. Mushnoori, M. Dutt and A.V. Tkachenko, The Journal of Chemical Physics (in press) (2022). [Paper] [Code]

A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. A. Banerjee, C. Y. Lu and M. Dutt, Physical Chemistry Chemical Physics (2022), 24, 1553-1568. [Paper] [Data] [Code]

Dendronized Vesicles: Formation, Self-organization of Dendron-grafted Amphiphiles and Stability. A. Banerjee, A. Tam and M. Dutt, Nanoscale Advances (2021), 3, 725-737. [Paper] [Data]

Peptide-based Vesicles and Droplets: A Review. S. Mushnoori, C. Y. Lu, K. Schmidt, E. Zang and M. Dutt, Journal of Physics: Condensed Matter (2020), 33, 053002. [Paper]

Implementation of Dynamic Coupling in Hybrid Molecular Dynamics-Lattice Boltzmann Approach: Modeling Aggregation of Amphiphiles Computer Physics Communications. X. Yu and M. Dutt, Computer Physics Communications (2020), DOI: 10.1016/j.cpc.2020.107287 [Paper] [Code]

Organization and Dynamics of Water on Titania Surfaces. S.C. Mushnoori, L. Chong and M. Dutt, MRS Advances (2019), 4 (5), 2717-2726. [Paper]

Computational Methods to Study Nanocomposites and Nanosuspensions for Heat Transfer Applications, Thermal Behavior and Applications in Carbon-based Materials. F. Aydin, X. Chu and M. Dutt, Eds. D. Papavassiliou, H. Duong and F. Gong, Elsevier (2019). (Book Chapter)

Dissipative Particle Dynamics Approaches to Modeling the Self-Assembly and Morphology of Neutral and Ionic Block Copolymers in Solution. T.A. Deaton, F. Aydin, N. Li, X. Chu, M. Dutt and Y. Yingling, Ed. E. Maginn, Molecular Modeling and Simulation, Applications and Perspectives (2019). (Book Chapter)

Structure and Phase Transitions of Two-Dimensional Core-Softened Colloidal Dumbbells: A Molecular Dynamics Study. Z. Yang, M. Dutt and Y. Chiew,Materials Research Express (2019), 6, 075076. [Paper]

A Multiscale Approach to Study Molecular and Interfacial Characteristics of Vesicles. X. Yu and M. Dutt, Molecular Systems Design & Engineering, 2018, DOI: 10.1039/C8ME00029H [Paper]

A review on phospholipid vesicles flowing through channels F. Aydin, X. Chu, J. Greenstein and M. Dutt, MRS Communications 2018. DOI: 10.1557/mrc.2018.118 [Paper]

Mechanisms underlying interactions between PAMAM dendron-grafted surfaces with DPPC membranes Jia Li, Kai Jin, Srinivas C. Mushnoori and Meenakshi Dutt, RSC Advances (2018), 8, 24982-24992. [Paper]

Designing Phenylalanine-based Hybrid Biological Materials: Controlling Morphology via Molecular Composition Srinivas C. Mushnoori, Kassandra Schmidt, Vikas Nanda and Meenakshi Dutt, Organic & Biomolecular Chemistry (2018), DOI: 10.1039/C8OB00130H [Paper]

Degree of unsaturation and backbone orientation of amphiphilic macromolecules influence local lipid properties in large unilamellar vesicles K. E. Uhrich, A. Moretti, B. Zhang, B. Lee, and M. Dutt. Langmuir 2017. DOI: 10.1021/acs.langmuir.7b03043 [Paper]

Flow-Induced Shape Reconfiguration, Phase Separation and Rupture of Bio-Inspired Vesicles X. Chu, X. Yu, J. Greenstein, F. Aydin, G. Uppaladadium and M. Dutt, ACS Nano 2017. DOI: 10.1021/acsnano.7b00753. [Paper]

Self-Assembly of Virus Capsids Decorated with Block Copolymers: A Simulation Study Dutt, Meenakshi; Chong, Leebyn; Libring, Sarah; Karra, Vyshnavi, Journal of Materials Research 2016. [Paper]

Modeling Interactions Between Multicomponent Vesicles and Anti-Microbial Peptide-Inspired Nanoparticles X. Chu, F. Aydin and M. Dutt, ACS Nano 2016, DOI: 10.1021/acsnano.5b08133. [Paper]

Surface Reconfiguration of Binary Lipid Vesicles Via Electrostatically-induced Nanoparticle Adsorption F. Aydin and M. Dutt, Journal of Physical Chemistry B 2016, DOI: 10.1021/acs.jpcb.6b02334. [Paper]

Self-Assembly and Critical Aggregation Concentration Measurements of ABA Triblock Copolymers with Varying B Block Types: Model Development, Prediction and Validation
F. Aydin*, X. Chu*, G. Upplaldadium*, D. Devore, R. Goyal, N. S. Murthy, Z. Zhang, J. Kohn and M. Dutt., Journal of Physical Chemistry B 2016, DOI: 10.1021/acs.jpcb.5b12594. [Paper]
* Equal contribution.

Harnessing Steric Hindrance to Control Interfacial Adsorption of Patchy Nanoparticles onto Hairy Vesicles
F. Aydin, G. Upplaldadium and M. Dutt., Bionterfaces 2016, DOI: 10.1016/j.colsurfb.2016.01.061. [Paper]

Molecular dynamics study of water over Pt/TiO2 Surfaces
S. Mushnoori, L. Chong and M. Dutt., Materials Today: Proceedings 3 (2016) pp. 513-517. [Paper]

Implicit Solvent Coarse-Grained Model of Polyamidoamine Dendrimers: Role of Generation and pH
L. Chong, F. Aydin and M. Dutt, Journal of Computational Chemistry 2015, DOI: 10.1002/jcc.24277 [Paper]

Interactions of Bio-Inspired Membranes with Peptides and Peptide-Mimetic Nanoparticles
Michael Sebastiano, Xiaolei Chu, Fikret Aydin, Leebyn Chong, and Meenakshi Dutt, AIMS Materials Science, Volume 2, Issue 3, 303-318. DOI: 10.3934/matersci.2015.3.303 [Paper]

Harnessing Nanoscale Confinement to Design Sterically Stable Vesicle
Fikret Aydin, Geetartha Uppaladadium and Meenakshi Dutt, Journal of Physical Chemistry B 2015. DOI: 10.1021/acs.jpcb.5b02239 [Paper]

Design of PAMAM-COO Dendron-Grafted Surfaces to Promote Pb(II) Ion Adsorption
Leebyn Chong and Meenakshi Dutt, Physical Chemistry Chemical Physics 2015. DOI: 10.1039/C5CP00309A [Paper]

The Design of Shape-Tunable Hairy Vesicles
Fikret Aydin, Geetartha Uppaladadium and Meenakshi Dutt, Colloids and Surfaces B: Biointerfaces 2015. DOI: 10.1016/j.colsurfb.2015.01.049 [Paper]

Designing Soft Nanomaterials via the Self Assembly of Functionalized Icosahedral Viral Capsid Nanoparticles
Vidyalakshmi Chockalingam Muthukumar, Leebyn Chong and Meenakshi Dutt, J. Materials Research 2014. DOI: 10.1557/jmr.2014.346 [Paper]

Computer Simulations of Fluid Flow over Catalytic Surfaces for Water Splitting
L. Chong, M. Dutt, Applied Surface Science 2014. DOI: 10.1016/j.apsusc.2014.08.172 [Paper]

Bioinspired Vesicles Encompassing Two-Tail Phospholipids: Self-Assembly and Phase Segregation via Implicit Solvent Coarse-Grained Molecular Dynamics
F. Aydin, M. Dutt, J. Phys. Chem. B 2014. DOI: 10.1021/jp503376r [Paper]

Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species
F. Aydin, P. Ludford, M. Dutt, Soft Matter 2014. DOI: 10.1039/C4SM00998C [Paper]

Computational Design of Multi-component Bio-Inspired Bilayer Membranes
E. Koufos, B. Muralidharan, M. Dutt, AIMS Press Materials Science 2014, 1(2), 103. doi:10.3934/matersci.2014.1.103 [Paper]

Granular Dynamics Simulations of the Effect of Grain Size Dispersity on Uniaxially Compacted Powder Blends
M. Dutt, J.A. Elliott, Granular Matter, DOI: 10.1007/s10035-013-0463-3. [Paper]

Nano-pipette directed transport of nanotube transmembrane channels and hybrid vesicles
M. Dutt, O. Kuksenok, A.C. Balazs, Nanoscale 2013, 5(20), 9773. DOI: 10.1039/C3NR33991B. [Paper]

Design of Nanostructured Hybrid Inorganic-biological Materials via Self-assembly
E. Koufos, M. Dutt, MRS Spring 2013 Conference Proceedings.

Design and Characterization of Nanostructured Biomaterials via the Self-assembly of Lipids
P. Ludford, F. Aydin, M. Dutt, MRS Fall 2012 Conference Proceedings.

Designing Tunable Bio-nanostructured Materials via Self-assembly of Amphiphilic Lipids and Functionalized Nanotubes
M. Dutt, O. Kuksenok, S.R. Little, A.C. Balazs, MRS Spring 2012 Conference Proceedings.

Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-organization
M. Dutt, M.J. Nayhouse, O. Kuksenok, S.R. Little, A.C. Balazs, special issue on Molecular Simulation of Nano-particle/ Lipid-Membrane Interactions in Current Nanoscience. (in press). [Paper]

Modeling of the Self-assembly of Lipids and Nanotubes in Solution: Forming Vesicles and Bicelles with Trans-Membrane Nanotube Channels
M. Dutt, O. Kuksenok, M.J.Nayhouse, S.R. Little, A.C. Balazs, ACS Nano 2011, DOI: 10.1021/nn201260r. [Paper]

Forming Trans-membrane Channels Using End-Functionalized Nanotubes
M. Dutt, O. Kuksenok, S.R. Little, A.C. Balazs, Nanoscale 2011, DOI: 10.1039/C0NR00578A. [Paper]

Numerical Model for Ultra-fine Particles in the Absence and Presence of Gravity
Meenakshi Dutt and J.A. Elliott, Powders and Grains 2009: Proceedings of the 6th International Conference on Micromechanics of Granular Media vol. 1145, p. 101 (2009). [Paper]

The Effect of Particle Size Dispersity in Dense Granular Packings on the Void Structure and the Interparticle Contact Frictional State
Meenakshi Dutt and J.A. Elliott, Powders and Grains 2009: Proceedings of the 6th International Conference on Micromechanics of Granular Media vol. 1145, p. 803 (2009). [Paper]

A Particle-Substrate Numerical Model for a quasi-2D Driven Dissipative Granular Gas
Meenakshi Dutt and R.P. Behringer, Powders and Grains 2009: Proceedings of the 6th International Conference on Micromechanics of Granular Media vol. 1145, p.1112 (2009). [Paper]

An extension of the DL\_POLY granular dynamics code to study ultra-fine particulate ensembles
M. Dutt, B.C. Hancock, A.C. Bentham, J.A. Elliott, submitted.

Influence of particle size dispersity on frictional frustration in dense compressed dense packings
M. Dutt, B. Hancock, C. Bentham, J. Elliott, submitted.

Dynamically Tessellating Algorithm for Analysis of Pore Size Distribution in Particle Agglomerates
M. Benedict, M. Dutt, J.A. Elliott, Physica A 378, 465 (2007). [Paper]

Effects of surface friction on a two-dimensional granular system: numerical model of a granular collider experiment
M. Dutt, R.P. Behringer, Physical Review E 75, 021305 (2007). [Paper]

Granular templating: effects of boundary structure on particle packings generated by simultaneous shear and compression
M. Dutt, B.C. Hancock, A.C. Bentham, J.A. Elliott, Europhysics Letters 77, 18001 (2007). [Paper]

Microstructural Studies of Dense Granular Media \& Their Importance to the Pharmaceutical Industry
M. Dutt, J.A. Elliott, International Congress of Industrial and Applied Mathematics 2007, Proceedings in Applied Mathematics and Mechanics (in press).

Applications of DL\_POLY to modeling of mesoscopic particulate systems
J.A. Elliott, M. Benedict, M. Dutt, Molecular Simulations 32, 1113 (2006). [pdf]

Investigation of particle packing in model pharmaceutical powders using x-ray microtomography and discrete element method
X.W. Fu, M. Dutt, A.C. Bentham, B.C. Hancock, R.E. Cameron, J. A. Elliott, Powder Technology 167, 134 (2006). [Paper]

An implementation of granular dynamics for simulating frictional elastic particles based on the DL_POLY code
M. Dutt, C. Bentham, B. Hancock, J. A. Elliott, Computer Physics Communications 166, 26 (2005). [Paper]

Quantitative analysis of packed and compacted granular system by X-ray microtomography
X.W. Fu, G.E. Milroy, M. Dutt, A.C. Bentham, B.C. Hancock, J.A. Elliott, Medical Imaging 2005: Image Processing, Proceedings of the Society of Photo-Optical Instrumentation Engineers (SPIE) 5747 Pt. 1-3, 1955-1964 (2005).

The Granular Collider: Particle-Substrate Model and the Numerical Experiment
M. Dutt, R.P. Behringer, Powders and Grains 2005, ed. R. Garcia-Rojo, H.J. Herrmann, S. McNamara, Balkema, Rotterdam, 2005.

Effects of Size Polydispersity on Pharmaceutical Particle Packings
C. Bentham, M. Dutt, B. Hancock, J. Elliott, Powders and Grains 2005, ed. R. Garcia-Rojo, H.J. Herrmann, S. McNamara, Balkema, Rotterdam, 2005.

Studies of Particle Packings in Mixtures of Pharmaceutical Excipients
M. Dutt, B. Hancock, C. Bentham, J. Elliott, Powders and Grains 2005, ed. R. Garcia-Rojo, H.J. Herrmann, S. McNamara, Balkema, Rotterdam, 2005.

Ordered Packing Induced by Simultaneous Shear and Compaction
B. Hancock, M. Dutt, C. Bentham, J. Elliott, Powders and Grains 2005, ed. R. Garcia-Rojo, H.J. Herrmann, S. McNamara, Balkema, Rotterdam, 2005.

Porosity Determination in Mesoscale Simulations using Artificial Intelligence Technique
M. Benedict, M. Dutt, J. Elliott, Proceedings of the Intelligent Processing and Manufacturing of Materials 2005.

Effects of Surface Friction on a Two Dimensional Granular System: Cooling Bound System
M. Dutt, R.P. Behringer, Physical Review E 70, 061304 (2004). [Paper]

Energy Dissipation and Clustering for a Cooling Granular Material on a Substrate
B. Painter, M. Dutt and R.P. Behringer, Physica D 175, 43 (2003). [Paper]

Please email me for preprints. email: meenakshi.dutt_at_rutgers.edu