Debashish Mukherji

Max Planck Institute for Polymer Research, Mayence, Rheinland-Pfalz, Germany

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Publications (27)65.27 Total impact

  • soon to be submitted. 07/2014;
  • Debashish Mukherji, Carlos M. Marques, Kurt Kremer
    in preparation. 07/2014;
  • Debashish Mukherji, Carlos M. Marques, Kurt Kremer
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    ABSTRACT: Water and alcohol, such as methanol or ethanol, are miscible and, individually, good solvents for several smart polymers, but this polymer precipitates in water-alcohol mixtures. The intriguing behavior of solvent mixtures that cannot dissolve a given polymer or a given protein, while the same macromolecule dissolves well in each of the cosolvents, is called cononsolvency. It is a widespread phenomenon, relevant for many formulation steps in the physicochemical and pharmaceutical industry, that is usually explained by invoking specific chemical details of the mixtures: as such it has so far eluded any generic explanation. Here, by using a combination of simulations and theory, we present a simple and universal treatment that requires only the preferential interaction of one of the cosolvents with the polymer. The results show striking quantitative agreement with experiments and chemically specific simulations, opening a new perspective towards an operational understanding of macromolecular solubility.
    Nature Communications 07/2014; 5:xxxx. · 10.74 Impact Factor
  • Debashish Mukherji, Kurt Kremer
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    ABSTRACT: Conformational transitions of (bio)macromolecules in aqueous mixtures are intimately linked to local concentration fluctuations of different solvent components. Though computer simulations are ideally suited to investigate such phenomena, in conventional setups the excess of one cosolvent close to the solute leads to depletion elsewhere, requiring very large simulations domain to avoid system size effects. We, here, propose an approach to overcome this depletion effect, which combines the Adaptive Resolution Scheme (AdResS) with a Metropolis particle exchange criterion. In AdResS, a small all-atom region, containing the solute, is coupled to a coarse-grained reservoir, where the particle exchange is performed. The particle exchange would be almost impossible had they been performed in an all-atom setup of a dense molecular liquid. We apply this approach to the reentrant collapse and swelling transition of poly(N-isopropylacrylamide) in aqueous methanol mixtures and demonstrate the role of the delicate interplay of the different intermolecular interactions.
    Macromolecules 11/2013; 46:9158. · 5.93 Impact Factor
  • Debashish Mukherji, Kurt Kremer
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    ABSTRACT: (Bio)macromolecular solvation in water cosolvent mixtures are dictated by the preferential interaction of cosolvents with the proteins. The numerical studies in the field are limited to the closed boundary schemes, which, however, suffers from severe system size effects. More specifically, when the conformational transitions are intimately linked to the large concentration fluctuations, the excess of cosolvents near a protein lead to depletion elsewhere in a small-sized closed boundary setup. This disturbs solvent equilibrium within the bulk solution. Therefore, by combining the adaptive resolution scheme (AdResS) with a metropolis particle exchange criterion, we propose a ``truly'' open boundary method that heals the particle depletion in a closed boundary setup. In AdResS, an all-atom region, containing protein, is coupled to a coarse-grained (CG) reservoir. Particle exchange is performed in the CG region, which otherwise would be impossible in an all-atom setup of dense fluids. We calculate solvation free energies within the all-atom region using Kirkwood-Buff theory. Our method produces well converged solvation energies that are impossible in a brute force all-atom MD of small system sizes. We will discuss two cases of triglycine in aqueous urea and PNIPAm in aqueous methanol.
    03/2013;
  • Debashish Mukherji, Kurt Kremer
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    ABSTRACT: Coupling different level of resolutions within a unified molecular dynamics scheme seeks to attain large time and length scale while retaining the full chemical detail only in the region of interest. One such multiscale technique is the adaptive resolution molecular dynamic scheme (AdResS). In AdResS, a high resolution all-atom region is coupled to a coarse-grained particle reservoir. Implementing the AdResS scheme, for the (bio)macromolecular simulations, is of particular importance, where the full chemical details are only important within a few nanometers from the solvated protein. The remaining solvent molecules, that are present to maintain equilibrium with the bulk solution, can be represented by single site coarse-grained beads. The coupling leads to correct concentration fluctuations within the small all-atom region, making the all-atom region an “effective” open boundary system. We treat this small all-atom region within the framework of fluctuation theory of Kirkwood and Buff, derived for open systems. We will present examples where this open boundary approach is successfully used to calculate solvation free energies of aqueous mixtures.
    03/2013: pages 111-125; , ISBN: 978-3-89336-849-5
  • Debashish Mukherji, Kurt Kremer
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    ABSTRACT: Coupling different levels of resolutions within a unified molecular dynamics scheme seeks to attain large time and length scale while keeping the full chemical detail in the region of high resolution. One such multi-scale technique is the adaptive resolution molecular dynamic scheme (AdResS). In AdResS, a high resolution all-atom region is coupled with a much larger coarse-grained particle reservoir, where particle exchange is allowed, on-the-fly, in thermodynamic equilibrium. Implementing this approach is of particular advantage when simulating solvation thermodynamics of biologically relevant aqueous mixtures. For example, coupling of high resolution all-atom system to a much larger osmotic coarse-grained region ensures a overall solvent equilibrium, which is extremely relevant in studying liquid mixtures. Therefore, the all-atom region can be considered as an “effective” open boundary. We treat this small all-atom region within the framework of fluctuation theory of Kirkwood and Buff. We will present examples where this open boundary approach can be efficiently implemented to study the aqueous mixtures.
    12/2012;
  • Source
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    ABSTRACT: We present molecular dynamics study of a generic (coarse-grained) model for single-polymer diffusion confined in a corrugated cylinder. For a narrow tube, i.e., diameter of the cylinder < 2.3, the axial diffusion coefficient D|| scales as D|| ~ N−3/2, with chain length N, up to N ~ 100 then crosses over to Rouse scaling for the larger N values. The N−3/2 scaling is due to the large fluctuation of the polymer chain along its fully stretched equilibrium conformation. The stronger scaling is not observed for an atomistically smooth tube and/or for a cylinder with larger diameter.
    The Journal of Chemical Physics 09/2012; 137:114902. · 3.12 Impact Factor
  • Debashish Mukherji, Nico F. A. van der Vegt, Kurt Kremer
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    ABSTRACT: Solvation free energies of peptides in water decrease with increasing urea concentration and therefore lead to increased solubility. In this work, we study the solvation thermodynamics of a tri-glycine in aqueous urea solution at room temperature T=300K. We perform our analysis within the framework of the Kirkwood-Buff theory of liquid mixtures, developed for open systems. For this purpose, we use a recently proposed approach to study liquid mixtures in an ``effective" open boundary simulation scheme (AdResS). We couple a small open boundary all-atom (explicit) region to a much larger coarse-grained particle reservoir. This coupling allows the free exchange of particles in thermodynamic equilibrium. Our approach preserves correct particle fluctuations that are important for studying the concentration driven conformational transition of (bio)molecules.
    Journal of Chemical Theory and Computation 07/2012; 8:3536. · 5.39 Impact Factor
  • Source
    Andres De Virgiliis, Debashish Mukherji
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    ABSTRACT: We present a molecular dynamics study of a generic (coarse-grained) model for single-polymer diffusion confined in a corrugated cylinder. The inherent structure of the cylinder is similar to that of a carbon nano-tube. For a narrow tube, i.e., radius of cylinder comparable to the size of the monomer, the axial diffusion coefficient $D_{||}$ scales as $D_{||} \propto N^{-3/2}$, with chain length $N$, up to $N \approx 100$ then crosses over to Rouse scaling for the larger $N$ values. The $N^{-3/2}$ scaling is due to the large fluctuation of polymer along its fully stretched equilibrium conformation. The stronger scaling is not observed for an atomistically smooth tube.
    submitted. 04/2012;
  • Debashish Mukherji, Nico F. A. van der Vegt, Kurt Kremer
    [Show abstract] [Hide abstract]
    ABSTRACT: Solvation free energies of peptides in water decrease with increasing urea concentration and therefore lead to increased solubility. In this work, we study the solvation thermodynamics of a tri-glycine in aqueous urea solution at room temperature T=300K. We perform our analysis within the framework of the Kirkwood-Buff theory of liquid mixtures, developed for open systems. For this purpose, we use a recently proposed approach to study liquid mixtures in an ``effective" open boundary simulation scheme (AdResS). We couple a small open boundary all-atom (explicit) region to a much larger coarse-grained particle reservoir. This coupling allows the free exchange of particles in thermodynamic equilibrium. Our approach preserves correct particle fluctuations that are important for studying the concentration driven conformational transition of (bio)molecules.
    Submitted. 03/2012;
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    ABSTRACT: We present an approach to systematically coarse-grain liquid mixtures using the fluctuation solution theory of Kirkwood and Buff in conjunction with the iterative Boltzmann inversion method. The approach preserves both the liquid structure at pair level and the dependence of solvation free energies on solvent composition within a unified coarse-graining framework. To test the robustness of our approach, we simulated urea–water and benzene–water systems at different concentrations. For urea–water, three different coarse-grained potentials were developed at different urea concentrations, in order to extend the simulations of urea–water mixtures up to 8 molar urea concentration. In spite of their inherent state point dependence, we find that the single-site models for urea and water are transferable in concentration windows of approximately 2 M. We discuss the development and application of these solvent models in coarse-grained biomolecular simulations.
    Journal of Chemical Theory and Computation 03/2012; 8:1802. · 5.39 Impact Factor
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    ABSTRACT: Using the adaptive resolution (AdResS) molecular dynamics scheme, we present a new approach to calculate the thermodynamic properties of liquid mixtures in an open boundary simulation. As a test case, we simulate methanol–water mixtures. We show that Kirkwood–Buff integrals (KBI), which directly connect global thermodynamic properties to microscopic molecular distributions, can be efficiently calculated over a wide range of methanol mole fractions by choosing only a very small (3% of total simulation domain) open boundary explicit (all atom) region and a surrounding coarse-grained reservoir that takes care of correct particle fluctuations.
    Journal of Chemical Theory and Computation 02/2012; 8(2):375. · 5.39 Impact Factor
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    ABSTRACT: Biological organizations depend on a sensitive balance of noncovalent interactions, in particular also those involving interactions of small molecules, including inorganic salts and urea, with biomolecules in aqueous solution. Computer simulations of these types of systems require simple-yet-specific models in order to cover all relevant time and length scales. We present a method to systematically coarse-grain liquid mixtures using Kirkwood-Buff theory of solution combined with an iterative Boltzmann inversion technique that infers single-site interaction potentials for the solution components from the pair correlation functions. Our method preserves both the solution structure at pair level and variations of solution components' chemical potentials with compositions within a unified coarse-graining framework. To test the robustness of our approach, we simulated urea-water and benzene-water systems over a wide-range of concentrations. We also observe the coarse-grained potentials to be reasonably transferable with varying concentrations.
    02/2012;
  • Source
    Andres De Virgiliis, Debashish Mukherji
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    ABSTRACT: We present a molecular dynamics study of a generic, coarse-grained model for single-polymer diffusion confined in a cylinder, which has variable atomic-scale roughness. Inherent structure of the cylinder is similar to that of a carbon nano-tube. For narrow tube, i.e., radius of cylinder comparable to the size of the monomer, the axial diffusion coefficient $D_{||}$ scales as $D_{||} \propto N^{-3/2}$, with chain length $N$, upto $N \approx 100$ then crosses over to Rouse scaling for the larger $N$ values. This strongly correlated dynamics is reminiscent of single file diffusion in a narrow channel.
    Journal name will be included when accepted. 01/2012;
  • will be shown later. 01/2012;
  • Debashish Mukherji, Martin H. Müser
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    ABSTRACT: Using molecular dynamics simulations, we study static and dynamic properties of isolated linear polymers in good solvent conditions, which are confined between two parallel, corrugated walls. If the distance between the confining walls is so small that the accessible space for a monomer, normal to the surface, is comparable to the monomer size itself, the diffusion constant $D$ is found to follow Rouse scaling, i.e., $D \approx N^{-1}$, with the degree of polymerization $N$. The proportionality constant is sensitive to wall-wall and wall-polymer commensurability. Upon further increasing the confinement (or decreasing the inter-wall distance) a stronger scaling is observed, where $D \approx N^{-3/2}$. Static properties, such as out-of-plane monomer density profile $n(z)$ and radius of gyration $R_{\rm g}$, obey the scaling laws predicted by Flory's mean field theory.
    SAIP 2011 Conference Series. 01/2011;
  • Debashish Mukherji, Cameron Abrams
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    ABSTRACT: Mechanical properties of highly cross-linked polymer (HCP) networks, e.g., thermosets, can be significantly modified by adding linear polymer chains, e.g., thermoplastics. In this work, we study thermoset/thermoplastic polymer alloys by means of large scale molecular dynamics simulations (MD) of a coarse-grained model. We focus here on the effect of linear chain mass fraction gammal, for different chain lengths Nl, and strain rates ε. Our results show that tensile strain (i.e; strain to break) decreases with increasing mass fraction gammal, up to a threshold value gammal^*, beyond which it increases with gammal. This non-monotonic behavior, which we call ``anomalous ductility", is qualitatively independent of ε and Nl, so long as fracture occurs in bulk. gammal^* decreases with increasing chain length and we observe microscopic evidence that this threshold value signifies the onset of interchain interactions. A simple scaling argument suggests that gammal^* is related to the overlap concentration of the thermoplastic homopolymer in the cured thermoset matrix.
    03/2010;
  • Debashish Mukherji, Cameron F. Abrams
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    ABSTRACT: Using large-scale molecular-dynamics simulation of a generic model, we study the mechanical behavior of thermoset/thermoplastic polymer alloys under shear. We investigate the effect of thermoplastic mass fraction Γl and the thermoplastic chain length Nl. Our results show two different fracture peaks in the stress-strain behavior. The first peak occurs at around 60% strain followed by a stress plateau, and the system fails at around 90% strain. This "slip-stick" fracture is independent of shear rate \dot{\varepsilon} and only occurs when Γl is less than the threshold concentration Γ* at which thermoplastic chains start to overlap. A micro-structural analysis suggests that the escape of thermoplastic chains from cavities near the fractured interfaces gives rise to slip-stick behavior. Slip-stick behavior has a strong chain length dependence and is only observed when Nl is greater than critical chain length Nlc=40. Slip-stick fracture makes an alloy of Γl=4.7% more than 40% tougher than a neat thermoset.
    EPL (Europhysics Letters) 01/2010; 90:26003. · 2.26 Impact Factor
  • Debashish Mukherji, Cameron F Abrams
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    ABSTRACT: Highly cross-linked polymer (HCP) networks are becoming increasingly important as high-performance adhesives and multifunctional composite materials. Because of their cross-linked molecular architectures, HCPs can be strong but brittle. One key goal in improving the performance of an HCP is to increase toughness without sacrificing strength. Using large scale molecular-dynamics simulation, we compare and characterize the mechanical behavior of two model HCPs under tensile deformation. In the first case, bond angles among any three connected monomers are unconstrained and in the second case we impose harmonic tetrahedral bond angle constraints. We perform a detailed microstructural analysis that establishes a unique correlation between macroscopic mechanical behavior and the microscopic structure of an HCP. While, in the unconstrained system, strain-hardening behavior is observed that is attributed to the formation of microvoids, the void growth is completely arrested in the constrained system and no strain hardening is observed. Moreover, after the initial strain-hardening phase, the unconstrained system displays the same stress-strain behavior as that of a constrained network. Strain hardening makes the unconstrained system ductile while it retains the same tensile strength as the constrained system. We suggest that bond angle flexibility of cross-linkers might be a possible means to control ductility in an HCP network at a constant cross-linker density. We have also studied the effect of temperature, strain rate, and intermonomer nonbonded interaction strength on the stress-strain behavior. Interestingly at a strong intermonomer nonbonded interaction strength, no strain hardening is observed even in the unconstrained system and fracture sets in at around 1% strain, similar to what is observed in an experimental system such as epoxy and vinyl-ester based thermosets. This indicates that strong nonbonded interactions play a key role in making an HCP strong but brittle.
    Physical Review E 07/2009; 79(6 Pt 1):061802. · 2.31 Impact Factor

Publication Stats

49 Citations
65.27 Total Impact Points

Institutions

  • 2012–2014
    • Max Planck Institute for Polymer Research
      Mayence, Rheinland-Pfalz, Germany
  • 2008–2009
    • Drexel University
      • Department of Chemical and Biological Engineering
      Philadelphia, PA, United States
  • 2006–2008
    • The University of Western Ontario
      • • Department of Applied Mathematics
      • • Department of Physics and Astronomy
      London, Ontario, Canada