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Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995.

Soft matter

van der Vegt NF, Rodríguez-Ropero F.
PMID: 28262864
Soft Matter. 2017 Mar 22;13(12):2289-2291. doi: 10.1039/c6sm02139e.

In a recent paper, Mukherji et al. describe the collapse of poly(N-isopropyl acrylamide) in methanol-water mixtures based on experiments and molecular dynamics simulations. The conclusion of their work is that chain collapse is dominated by enthalpic bridging interactions while...

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van der Vegt NF, Rodríguez-Ropero F. Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995. Soft Matter. 2017;13(12):2289-2291doi: 10.1039/c6sm02139e.
van der Vegt, N. F., & Rodríguez-Ropero, F. (2017). Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995. Soft matter, 13(12), 2289-2291. https://doi.org/10.1039/c6sm02139e
van der Vegt, Nico F A, and Rodríguez-Ropero, Francisco. "Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995." Soft matter vol. 13,12 (2017): 2289-2291. doi: https://doi.org/10.1039/c6sm02139e
van der Vegt NF, Rodríguez-Ropero F. Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995. Soft Matter. 2017 Mar 22;13(12):2289-2291. doi: 10.1039/c6sm02139e. PMID: 28262864.
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High sensitivity and negative predictive value of sentinel lymph node biopsy in a retrospective early stage oral cavity cancer cohort in the Northern Netherlands.

Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery

Boeve K, Schepman KP, Schuuring E, Roodenburg JLN, Halmos GB, van Dijk BAC, Boorsma RAC, de Visscher JGAM, Brouwers AH, van der Vegt B, Witjes MJH.
PMID: 29575685
Clin Otolaryngol. 2018 Aug;43(4):1080-1087. doi: 10.1111/coa.13107. Epub 2018 Apr 19.

OBJECTIVES: In cT1-2N0, oral squamous cell carcinoma (OSCC) occult metastases are detected in 23%-37% of cases. Sentinel lymph node biopsy (SLNB) was introduced in head and neck cancer as a minimally invasive alternative for an elective neck dissection in...

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Boeve K, Schepman KP, Schuuring E, et al. High sensitivity and negative predictive value of sentinel lymph node biopsy in a retrospective early stage oral cavity cancer cohort in the Northern Netherlands. Clin Otolaryngol. 2018;43(4):1080-1087doi: 10.1111/coa.13107.
Boeve, K., Schepman, K. P., Schuuring, E., Roodenburg, J. L. N., Halmos, G. B., van Dijk, B. A. C., Boorsma, R. A. C., de Visscher, J. G. A. M., Brouwers, A. H., van der Vegt, B., & Witjes, M. J. H. (2018). High sensitivity and negative predictive value of sentinel lymph node biopsy in a retrospective early stage oral cavity cancer cohort in the Northern Netherlands. Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery, 43(4), 1080-1087. https://doi.org/10.1111/coa.13107
Boeve, K, et al. "High sensitivity and negative predictive value of sentinel lymph node biopsy in a retrospective early stage oral cavity cancer cohort in the Northern Netherlands." Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery vol. 43,4 (2018): 1080-1087. doi: https://doi.org/10.1111/coa.13107
Boeve K, Schepman KP, Schuuring E, Roodenburg JLN, Halmos GB, van Dijk BAC, Boorsma RAC, de Visscher JGAM, Brouwers AH, van der Vegt B, Witjes MJH. High sensitivity and negative predictive value of sentinel lymph node biopsy in a retrospective early stage oral cavity cancer cohort in the Northern Netherlands. Clin Otolaryngol. 2018 Aug;43(4):1080-1087. doi: 10.1111/coa.13107. Epub 2018 Apr 19. PMID: 29575685.
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Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions.

Journal of chemical theory and computation

Ganguly P, Mukherji D, Junghans C, van der Vegt NF.
PMID: 26593671
J Chem Theory Comput. 2012 May 08;8(5):1802-7. doi: 10.1021/ct3000958. Epub 2012 Apr 02.

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...

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Ganguly P, Mukherji D, Junghans C, et al. Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions. J Chem Theory Comput. 2012;8(5):1802-7doi: 10.1021/ct3000958.
Ganguly, P., Mukherji, D., Junghans, C., & van der Vegt, N. F. (2012). Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions. Journal of chemical theory and computation, 8(5), 1802-7. https://doi.org/10.1021/ct3000958
Ganguly, Pritam, et al. "Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions." Journal of chemical theory and computation vol. 8,5 (2012): 1802-7. doi: https://doi.org/10.1021/ct3000958
Ganguly P, Mukherji D, Junghans C, van der Vegt NF. Kirkwood-Buff Coarse-Grained Force Fields for Aqueous Solutions. J Chem Theory Comput. 2012 May 08;8(5):1802-7. doi: 10.1021/ct3000958. Epub 2012 Apr 02. PMID: 26593671.
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Publisher's Note: "Solvation thermodynamics of amino acid side chains on a short peptide backbone" [J. Chem. Phys. 142, 144502 (2015)].

The Journal of chemical physics

Hajari T, van der Vegt NF.
PMID: 25933792
J Chem Phys. 2015 Apr 28;142(16):169901. doi: 10.1063/1.4919029.

No abstract available.

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Hajari T, van der Vegt NF. Publisher's Note: "Solvation thermodynamics of amino acid side chains on a short peptide backbone" [J. Chem. Phys. 142, 144502 (2015)]. J Chem Phys. 2015;142(16):169901doi: 10.1063/1.4919029.
Hajari, T., & van der Vegt, N. F. (2015). Publisher's Note: "Solvation thermodynamics of amino acid side chains on a short peptide backbone" [J. Chem. Phys. 142, 144502 (2015)]. The Journal of chemical physics, 142(16), 169901. https://doi.org/10.1063/1.4919029
Hajari, Timir, and van der Vegt, Nico F A. "Publisher's Note: "Solvation thermodynamics of amino acid side chains on a short peptide backbone" [J. Chem. Phys. 142, 144502 (2015)]." The Journal of chemical physics vol. 142,16 (2015): 169901. doi: https://doi.org/10.1063/1.4919029
Hajari T, van der Vegt NF. Publisher's Note: "Solvation thermodynamics of amino acid side chains on a short peptide backbone" [J. Chem. Phys. 142, 144502 (2015)]. J Chem Phys. 2015 Apr 28;142(16):169901. doi: 10.1063/1.4919029. PMID: 25933792.
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Mechanism of Polymer Collapse in Miscible Good Solvents.

The journal of physical chemistry. B

Rodríguez-Ropero F, Hajari T, van der Vegt NF.
PMID: 26619003
J Phys Chem B. 2015 Dec 24;119(51):15780-8. doi: 10.1021/acs.jpcb.5b10684. Epub 2015 Dec 10.

We propose a physical mechanism for co-nonsolvency of a stimulus-responsive polymer in water/methanol mixed solution based on results obtained with molecular simulations. Even though the phenomenon is well known, the mechanism behind co-nonsolvency is still under debate. Herein, we...

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Rodríguez-Ropero F, Hajari T, van der Vegt NF. Mechanism of Polymer Collapse in Miscible Good Solvents. J Phys Chem B. 2015;119(51):15780-8doi: 10.1021/acs.jpcb.5b10684.
Rodríguez-Ropero, F., Hajari, T., & van der Vegt, N. F. (2015). Mechanism of Polymer Collapse in Miscible Good Solvents. The journal of physical chemistry. B, 119(51), 15780-8. https://doi.org/10.1021/acs.jpcb.5b10684
Rodríguez-Ropero, Francisco, et al. "Mechanism of Polymer Collapse in Miscible Good Solvents." The journal of physical chemistry. B vol. 119,51 (2015): 15780-8. doi: https://doi.org/10.1021/acs.jpcb.5b10684
Rodríguez-Ropero F, Hajari T, van der Vegt NF. Mechanism of Polymer Collapse in Miscible Good Solvents. J Phys Chem B. 2015 Dec 24;119(51):15780-8. doi: 10.1021/acs.jpcb.5b10684. Epub 2015 Dec 10. PMID: 26619003.
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From Hydrophobic to Hydrophilic Solvation:  An Application to Hydration of Benzene.

Journal of chemical theory and computation

Schravendijk P, van der Vegt NF.
PMID: 26641686
J Chem Theory Comput. 2005 Jul;1(4):643-52. doi: 10.1021/ct049841c.

We report a computer simulation study on the hydration of benzene, which, despite being hydrophobic, is a weak hydrogen bond acceptor. The effect of benzene-water hydrogen bonding on the hydration free energy has been analyzed in terms of solute-solvent...

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Schravendijk P, van der Vegt NF. From Hydrophobic to Hydrophilic Solvation:  An Application to Hydration of Benzene. J Chem Theory Comput. 2005;1(4):643-52doi: 10.1021/ct049841c.
Schravendijk, P., & van der Vegt, N. F. (2005). From Hydrophobic to Hydrophilic Solvation:  An Application to Hydration of Benzene. Journal of chemical theory and computation, 1(4), 643-52. https://doi.org/10.1021/ct049841c
Schravendijk, Pim, and van der Vegt, Nico F A. "From Hydrophobic to Hydrophilic Solvation:  An Application to Hydration of Benzene." Journal of chemical theory and computation vol. 1,4 (2005): 643-52. doi: https://doi.org/10.1021/ct049841c
Schravendijk P, van der Vegt NF. From Hydrophobic to Hydrophilic Solvation:  An Application to Hydration of Benzene. J Chem Theory Comput. 2005 Jul;1(4):643-52. doi: 10.1021/ct049841c. PMID: 26641686.
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Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene.

Langmuir : the ACS journal of surfaces and colloids

Taherian F, Leroy F, Heim LO, Bonaccurso E, van der Vegt NF.
PMID: 26652691
Langmuir. 2016 Jan 12;32(1):140-50. doi: 10.1021/acs.langmuir.5b04161. Epub 2015 Dec 22.

The electrowetting behavior of 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) confined between two oppositely charged graphene layers is investigated using molecular dynamics simulations. By introducing charges on the surface, counterions are attracted to the surface and co-ions are repelled from it, leading...

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Taherian F, Leroy F, Heim LO, et al. Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene. Langmuir. 2015;32(1):140-50doi: 10.1021/acs.langmuir.5b04161.
Taherian, F., Leroy, F., Heim, L. O., Bonaccurso, E., & van der Vegt, N. F. (2016). Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene. Langmuir : the ACS journal of surfaces and colloids, 32(1), 140-50. https://doi.org/10.1021/acs.langmuir.5b04161
Taherian, Fereshte, et al. "Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene." Langmuir : the ACS journal of surfaces and colloids vol. 32,1 (2016): 140-50. doi: https://doi.org/10.1021/acs.langmuir.5b04161
Taherian F, Leroy F, Heim LO, Bonaccurso E, van der Vegt NF. Mechanism for Asymmetric Nanoscale Electrowetting of an Ionic Liquid on Graphene. Langmuir. 2016 Jan 12;32(1):140-50. doi: 10.1021/acs.langmuir.5b04161. Epub 2015 Dec 22. PMID: 26652691.
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Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method.

The Journal of chemical physics

Ardham VR, Deichmann G, van der Vegt NF, Leroy F.
PMID: 26723620
J Chem Phys. 2015 Dec 28;143(24):243135. doi: 10.1063/1.4936253.

We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic...

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Ardham VR, Deichmann G, van der Vegt NF, et al. Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method. J Chem Phys. 2015;143(24):243135doi: 10.1063/1.4936253.
Ardham, V. R., Deichmann, G., van der Vegt, N. F., & Leroy, F. (2015). Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method. The Journal of chemical physics, 143(24), 243135. https://doi.org/10.1063/1.4936253
Ardham, Vikram Reddy, et al. "Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method." The Journal of chemical physics vol. 143,24 (2015): 243135. doi: https://doi.org/10.1063/1.4936253
Ardham VR, Deichmann G, van der Vegt NF, Leroy F. Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method. J Chem Phys. 2015 Dec 28;143(24):243135. doi: 10.1063/1.4936253. PMID: 26723620.
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Osmotic coefficients of atomistic NaCl (aq) force fields.

The Journal of chemical physics

Hess B, Holm C, van der Vegt N.
PMID: 16674148
J Chem Phys. 2006 Apr 28;124(16):164509. doi: 10.1063/1.2185105.

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and...

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Hess B, Holm C, van der Vegt N. Osmotic coefficients of atomistic NaCl (aq) force fields. J Chem Phys. 2006;124(16):164509doi: 10.1063/1.2185105.
Hess, B., Holm, C., & van der Vegt, N. (2006). Osmotic coefficients of atomistic NaCl (aq) force fields. The Journal of chemical physics, 124(16), 164509. https://doi.org/10.1063/1.2185105
Hess, Berk, et al. "Osmotic coefficients of atomistic NaCl (aq) force fields." The Journal of chemical physics vol. 124,16 (2006): 164509. doi: https://doi.org/10.1063/1.2185105
Hess B, Holm C, van der Vegt N. Osmotic coefficients of atomistic NaCl (aq) force fields. J Chem Phys. 2006 Apr 28;124(16):164509. doi: 10.1063/1.2185105. PMID: 16674148.
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Modeling of molecular packing and conformation in oligofluorenes.

The journal of physical chemistry. B

Marcon V, van der Vegt N, Wegner G, Raos G.
PMID: 16539455
J Phys Chem B. 2006 Mar 23;110(11):5253-61. doi: 10.1021/jp056858y.

We describe the application of molecular modeling to study problems related to the packing and conformation of oligofluorene molecules in the solid state. First of all, we describe an improved force field for oligofluorenes. The model is based on...

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Marcon V, van der Vegt N, Wegner G, et al. Modeling of molecular packing and conformation in oligofluorenes. J Phys Chem B. 2006;110(11):5253-61doi: 10.1021/jp056858y.
Marcon, V., van der Vegt, N., Wegner, G., & Raos, G. (2006). Modeling of molecular packing and conformation in oligofluorenes. The journal of physical chemistry. B, 110(11), 5253-61. https://doi.org/10.1021/jp056858y
Marcon, Valentina, et al. "Modeling of molecular packing and conformation in oligofluorenes." The journal of physical chemistry. B vol. 110,11 (2006): 5253-61. doi: https://doi.org/10.1021/jp056858y
Marcon V, van der Vegt N, Wegner G, Raos G. Modeling of molecular packing and conformation in oligofluorenes. J Phys Chem B. 2006 Mar 23;110(11):5253-61. doi: 10.1021/jp056858y. PMID: 16539455.
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Atomic Structure of the c(4 x 2) Surface Reconstruction of Ge(001) as Determined by X-Ray Diffraction.

Physical review letters

Etgens VH, Fajardo P, Ferrer S, Torrelles X, van der Vegt HA.
PMID: 10060387
Phys Rev Lett. 1995 Aug 28;75(9):1771-1774. doi: 10.1103/PhysRevLett.75.1771.

No abstract available.

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Etgens VH, Fajardo P, Ferrer S, et al. Atomic Structure of the c(4 x 2) Surface Reconstruction of Ge(001) as Determined by X-Ray Diffraction. Phys Rev Lett. 1995;75(9):1771-1774doi: 10.1103/PhysRevLett.75.1771.
Etgens, V. H., Fajardo, P., Ferrer, S., Torrelles, X., & van der Vegt HA. (1995). Atomic Structure of the c(4 x 2) Surface Reconstruction of Ge(001) as Determined by X-Ray Diffraction. Physical review letters, 75(9), 1771-1774. https://doi.org/10.1103/PhysRevLett.75.1771
Etgens, et al. "Atomic Structure of the c(4 x 2) Surface Reconstruction of Ge(001) as Determined by X-Ray Diffraction." Physical review letters vol. 75,9 (1995): 1771-1774. doi: https://doi.org/10.1103/PhysRevLett.75.1771
Etgens VH, Fajardo P, Ferrer S, Torrelles X, van der Vegt HA. Atomic Structure of the c(4 x 2) Surface Reconstruction of Ge(001) as Determined by X-Ray Diffraction. Phys Rev Lett. 1995 Aug 28;75(9):1771-1774. doi: 10.1103/PhysRevLett.75.1771. PMID: 10060387.
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Disordering of the low-temperature c(4 x 2) structure of Ge(001) to the (2 x 1) reconstruction: Evidence for a mean-field transition.

Physical review. B, Condensed matter

Alvarez J, Etgens VH, Fajardo P, Ferrer S, Torrelles X, van der Vegt HA.
PMID: 9986521
Phys Rev B Condens Matter. 1996 Aug 15;54(8):5581-5585. doi: 10.1103/physrevb.54.5581.

No abstract available.

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Alvarez J, Etgens VH, Fajardo P, et al. Disordering of the low-temperature c(4 x 2) structure of Ge(001) to the (2 x 1) reconstruction: Evidence for a mean-field transition. Phys Rev B Condens Matter. 1996;54(8):5581-5585doi: 10.1103/physrevb.54.5581.
Alvarez, J., Etgens, V. H., Fajardo, P., Ferrer, S., Torrelles, X., & van der Vegt HA. (1996). Disordering of the low-temperature c(4 x 2) structure of Ge(001) to the (2 x 1) reconstruction: Evidence for a mean-field transition. Physical review. B, Condensed matter, 54(8), 5581-5585. https://doi.org/10.1103/physrevb.54.5581
Alvarez, et al. "Disordering of the low-temperature c(4 x 2) structure of Ge(001) to the (2 x 1) reconstruction: Evidence for a mean-field transition." Physical review. B, Condensed matter vol. 54,8 (1996): 5581-5585. doi: https://doi.org/10.1103/physrevb.54.5581
Alvarez J, Etgens VH, Fajardo P, Ferrer S, Torrelles X, van der Vegt HA. Disordering of the low-temperature c(4 x 2) structure of Ge(001) to the (2 x 1) reconstruction: Evidence for a mean-field transition. Phys Rev B Condens Matter. 1996 Aug 15;54(8):5581-5585. doi: 10.1103/physrevb.54.5581. PMID: 9986521.
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Showing 1 to 12 of 87 entries