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Kunche L, Natarajan U. Conformations and Solvation of Synthetic Polymers in Water by Generalized Born Implicit-Solvent Molecular Dynamics Simulations: Stereoisomers of Poly(acrylic acid) and Poly(methacrylic acid). J Phys Chem B 2023; 127:1244-1253. [PMID: 36705523 DOI: 10.1021/acs.jpcb.2c06658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present the GB-OBC model as an approach for implicit-solvent MD simulations of a synthetic macromolecule in water. The model is tested and found to be successful in reproducing the chain dimensions and predicting the free energy of solvation of carboxylic acid vinyl polymers. The influence of stereochemistry and the hydrophobic nature of the polymer was investigated as a function of chain length (20 < N < 600) for poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMA). The dimensionless parameters of the GB-OBC model were parameterized to be applicable to PAA and PMA. Scaling relations for chain dimensions obtained using implicit-solvent MD simulations in this study are in good agreement with those from experiments, theory of solvated chains in good solvents, and all-atom MD simulations in explicit water. Results show that ⟨Rg2⟩/NL2 is greater for the atactic chain as compared to the isotactic chain, for PAA as well as PMA. ⟨Rg2⟩/NL2 values of chains attain constancy in water for N = 200, with the values being greater for PMA. The PMA chain is conformationally more perturbed than the PAA chain, for both isotactic and atactic stereochemistry. The solvation free energy ΔGhyd of PAA and PMA in water is negative for all chain lengths (N = 20-600) and becomes more favorable with an increase in molecular weight. The ΔGhyd values for isotactic and atactic chains are identical at lower values of N but differ slightly for N > 300. Irrespective of the hydrophobic nature of the polymer, the atactic chain is thermodynamically more soluble in water as compared to the isotactic chain. The isotactic chain is less hydrophilic as compared to the atactic chain due to the closer proximity of the COOH groups along the backbone. This implicit solvent method is an effective way to accurately simulate the configurational properties and solvation of synthetic polymers in water.
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Affiliation(s)
- Lakshmikumar Kunche
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai600036, India
| | - Upendra Natarajan
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai600036, India
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Zhou Y, Latinwo F, Schroeder CM. Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis. ENTROPY (BASEL, SWITZERLAND) 2021; 24:27. [PMID: 35052053 PMCID: PMC8774537 DOI: 10.3390/e24010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022]
Abstract
Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.
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Affiliation(s)
- Yuecheng Zhou
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Folarin Latinwo
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Charles M. Schroeder
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
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Dinic J, Sharma V. Flexibility, Extensibility, and Ratio of Kuhn Length to Packing Length Govern the Pinching Dynamics, Coil-Stretch Transition, and Rheology of Polymer Solutions. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00076] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jelena Dinic
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60608, United States
| | - Vivek Sharma
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60608, United States
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Haward SJ. Characterization of hyaluronic acid and synovial fluid in stagnation point elongational flow. Biopolymers 2016; 101:287-305. [PMID: 23868350 DOI: 10.1002/bip.22357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
Hyaluronic acid (HA) is an important biomacromolecule, which fulfils a number of vital physiological functions (especially in the joint synovial fluid) and also has consumer and pharmaceutical applications. HA solution properties have already been quite thoroughly characterized in response to steady shear flows but are less well understood in highly deforming extensional flows. In this study, flow-induced birefringence measurements are made as a function of the strain rate in planar elongational flow at the stagnation point of a cross-slot device using HA solutions of a range of molecular weights (0.9×10(6) g mol(-1)≤Mw≤4.8×10(6) g mol(-1)) and at dilute concentrations. The results provide macromolecular relaxation times, molecular weight distributions and the extensional viscosities and Trouton ratios of the fluids. The HA relaxation time is found to vary as τ∼Mw1.8, which is consistent with a partially solvated, expanded coil. An intrinsic Trouton ratio is defined, which varies as [Tr]∼Mw2. The measurement of birefringence with strain rate is shown to be highly sensitive to the molecular weight distribution and can resolve subtle changes due to macromolecular degradation and the presence of fracture products. Mechanical degradation experiments in the cross-slots indicate midchain scission of HA macromolecules, strongly suggesting near full extension of the high-molecular weight fraction in the stagnation point extensional flow field. Taken together the results suggest a possible method for analysis of the HA in synovial fluid, and this concept is tested using synovial fluid obtained from porcine tarsal joint.
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Affiliation(s)
- Simon J Haward
- Departamento de Engenharia Química, CEFT, Faculdade de Engenharia da Universidade do Porto, Rua Dr Roberto Frias s/n, 4200-465 Porto, Portugal
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Klepinger AC, Greenier MK, Levy SL. Stretching DNA Molecules in Strongly Confining Nanofluidic Slits. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01712] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Madeline K. Greenier
- Department
of Physics, Binghamton University, Binghamton, New York 13902, United States
| | - Stephen L. Levy
- Department
of Physics, Binghamton University, Binghamton, New York 13902, United States
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Pandey H, Underhill PT. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052301. [PMID: 26651689 DOI: 10.1103/physreve.92.052301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 06/05/2023]
Abstract
The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.
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Affiliation(s)
- Harsh Pandey
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Patrick T Underhill
- The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Kurganov AA, Svec F, Kanateva AY. Flow induced conformational transitions of macromolecules and their effect on chromatographic separations. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kurganov AA, Kanateva AY, Orekhov VA. Conformational transitions of macromolecules in an eluent flow and their manifestation in the chromatography of polymers. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n07abeh004433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Latinwo F, Schroeder CM. Determining elasticity from single polymer dynamics. SOFT MATTER 2014; 10:2178-87. [PMID: 24651921 PMCID: PMC3966029 DOI: 10.1039/c3sm52042k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ability to determine polymer elasticity and force-extension relations from polymer dynamics in flow has been challenging, mainly due to difficulties in relating equilibrium properties such as free energy to far-from-equilibrium processes. In this work, we determine polymer elasticity from the dynamic properties of polymer chains in fluid flow using recent advances in statistical mechanics. In this way, we obtain the force-extension relation for DNA from single molecule measurements of polymer dynamics in flow without the need for optical tweezers or bead tethers. We further employ simulations to demonstrate the practicality and applicability of this approach to the dynamics of complex fluids. We investigate the effects of flow type on this analysis method, and we develop scaling laws to relate the work relation to bulk polymer viscometric functions. Taken together, our results show that nonequilibrium work relations can play a key role in the analysis of soft material dynamics.
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Affiliation(s)
- Folarin Latinwo
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Radhakrishnan R, Underhill PT. Fluctuations in the coil-stretch transition of flexible polymers in good solvents: a peak due to nonlinear force relation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012606. [PMID: 23944485 DOI: 10.1103/physreve.88.012606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/11/2013] [Indexed: 06/02/2023]
Abstract
Long flexible polymers undergo a coil to stretch transition (CST) in an elongational flow. Near the CST, a peak can be observed in the fluctuations of the size of a molecule (|R|). Solvent effects on the fluctuations are studied using Brownian dynamics simulations of a nonlinear spring force relation that can represent real molecules. Ignoring the influence of hydrodynamic interactions, a linear region in the spring force relation is known to cause the peak in |R| fluctuations. In contrast, we find that a peak in the fluctuations can be obtained even for the nonlinear spring force relation. We analyze the influence of hydrodynamic interactions on the fluctuations using a dumbbell model with a conformation-dependent drag coefficient.
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Affiliation(s)
- Rangarajan Radhakrishnan
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180, USA
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