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Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile.

Journal of chemical theory and computation

den Otter WK.
PMID: 26592381
J Chem Theory Comput. 2013 Sep 10;9(9):3861-5. doi: 10.1021/ct400134d. Epub 2013 Aug 26.

Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York [J. Chem. Theory...

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den Otter WK. Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile. J Chem Theory Comput. 2013;9(9):3861-5doi: 10.1021/ct400134d.
den Otter, W. K. (2013). Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile. Journal of chemical theory and computation, 9(9), 3861-5. https://doi.org/10.1021/ct400134d
den Otter, Wouter K. "Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile." Journal of chemical theory and computation vol. 9,9 (2013): 3861-5. doi: https://doi.org/10.1021/ct400134d
den Otter WK. Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile. J Chem Theory Comput. 2013 Sep 10;9(9):3861-5. doi: 10.1021/ct400134d. Epub 2013 Aug 26. PMID: 26592381.
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Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations.

The Journal of chemical physics

Tolpekina TV, den Otter WK, Briels WJ.
PMID: 15634170
J Chem Phys. 2004 Dec 15;121(23):12060-6. doi: 10.1063/1.1815296.

The formation of a pore in a membrane requires a considerable rearrangement of the amphiphilic molecules about to form the bilayer edge surrounding the pore, and hence is accompanied by a steep increase of the free energy. Recent rupture...

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Tolpekina TV, den Otter WK, Briels WJ. Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations. J Chem Phys. 2004;121(23):12060-6doi: 10.1063/1.1815296.
Tolpekina, T. V., den Otter, W. K., & Briels, W. J. (2004). Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations. The Journal of chemical physics, 121(23), 12060-6. https://doi.org/10.1063/1.1815296
Tolpekina, T V, et al. "Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations." The Journal of chemical physics vol. 121,23 (2004): 12060-6. doi: https://doi.org/10.1063/1.1815296
Tolpekina TV, den Otter WK, Briels WJ. Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations. J Chem Phys. 2004 Dec 15;121(23):12060-6. doi: 10.1063/1.1815296. PMID: 15634170.
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Mathematical analysis of the cellular immune reaction against tumour cells.

Immunology today

De Weger RA, Dullens HF, De Boer RJ, Den Otter W.
PMID: 25290993
Immunol Today. 1985 Nov;6(11):316-7. doi: 10.1016/0167-5699(85)90119-7.

No abstract available.

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De Weger RA, Dullens HF, De Boer RJ, et al. Mathematical analysis of the cellular immune reaction against tumour cells. Immunol Today. 1985;6(11):316-7doi: 10.1016/0167-5699(85)90119-7.
De Weger, R. A., Dullens, H. F., De Boer, R. J., & Den Otter, W. (1985). Mathematical analysis of the cellular immune reaction against tumour cells. Immunology today, 6(11), 316-7. https://doi.org/10.1016/0167-5699(85)90119-7
De Weger, R A, et al. "Mathematical analysis of the cellular immune reaction against tumour cells." Immunology today vol. 6,11 (1985): 316-7. doi: https://doi.org/10.1016/0167-5699(85)90119-7
De Weger RA, Dullens HF, De Boer RJ, Den Otter W. Mathematical analysis of the cellular immune reaction against tumour cells. Immunol Today. 1985 Nov;6(11):316-7. doi: 10.1016/0167-5699(85)90119-7. PMID: 25290993.
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Coarse grain forces in star polymer melts.

Soft matter

Liu L, den Otter WK, Briels WJ.
PMID: 25158294
Soft Matter. 2014 Oct 21;10(39):7874-86. doi: 10.1039/c4sm00767k. Epub 2014 Aug 26.

An analysis is presented of forces acting on the centers of mass of three-armed star polymers in the molten state. The arms consist of 35 Kremer-Grest beads, which is slightly larger than needed for one entanglement mass. For a...

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Liu L, den Otter WK, Briels WJ. Coarse grain forces in star polymer melts. Soft Matter. 2014;10(39):7874-86doi: 10.1039/c4sm00767k.
Liu, L., den Otter, W. K., & Briels, W. J. (2014). Coarse grain forces in star polymer melts. Soft matter, 10(39), 7874-86. https://doi.org/10.1039/c4sm00767k
Liu, L, et al. "Coarse grain forces in star polymer melts." Soft matter vol. 10,39 (2014): 7874-86. doi: https://doi.org/10.1039/c4sm00767k
Liu L, den Otter WK, Briels WJ. Coarse grain forces in star polymer melts. Soft Matter. 2014 Oct 21;10(39):7874-86. doi: 10.1039/c4sm00767k. Epub 2014 Aug 26. PMID: 25158294.
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Diaphragm-Based Position Verification to Improve Daily Target Dose Coverage in Proton and Photon Radiation Therapy Treatment of Distal Esophageal Cancer.

International journal of radiation oncology, biology, physics

Visser S, den Otter LA, Ribeiro CO, Korevaar EW, Both S, Langendijk JA, Muijs CT, Sijtsema NM, Knopf A.
PMID: 34530091
Int J Radiat Oncol Biol Phys. 2021 Sep 14; doi: 10.1016/j.ijrobp.2021.09.015. Epub 2021 Sep 14.

PURPOSE: In modern conformal radiation therapy of distal esophageal cancer, target coverage can be affected by variations in the diaphragm position. We investigated if daily position verification (PV) extended by a diaphragm position correction would optimize target dose coverage...

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Visser S, den Otter LA, Ribeiro CO, et al. Diaphragm-Based Position Verification to Improve Daily Target Dose Coverage in Proton and Photon Radiation Therapy Treatment of Distal Esophageal Cancer. Int J Radiat Oncol Biol Phys. 2021;doi: 10.1016/j.ijrobp.2021.09.015.
Visser, S., den Otter, L. A., Ribeiro, C. O., Korevaar, E. W., Both, S., Langendijk, J. A., Muijs, C. T., Sijtsema, N. M., & Knopf, A. (2021). Diaphragm-Based Position Verification to Improve Daily Target Dose Coverage in Proton and Photon Radiation Therapy Treatment of Distal Esophageal Cancer. International journal of radiation oncology, biology, physics, . https://doi.org/10.1016/j.ijrobp.2021.09.015
Visser, Sabine, et al. "Diaphragm-Based Position Verification to Improve Daily Target Dose Coverage in Proton and Photon Radiation Therapy Treatment of Distal Esophageal Cancer." International journal of radiation oncology, biology, physics vol. (2021). doi: https://doi.org/10.1016/j.ijrobp.2021.09.015
Visser S, den Otter LA, Ribeiro CO, Korevaar EW, Both S, Langendijk JA, Muijs CT, Sijtsema NM, Knopf A. Diaphragm-Based Position Verification to Improve Daily Target Dose Coverage in Proton and Photon Radiation Therapy Treatment of Distal Esophageal Cancer. Int J Radiat Oncol Biol Phys. 2021 Sep 14; doi: 10.1016/j.ijrobp.2021.09.015. Epub 2021 Sep 14. PMID: 34530091.
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Prediction of obstructive sleep apnea: comparative performance of three screening instruments on the apnea-hypopnea index and the oxygen desaturation index.

Sleep & breathing = Schlaf & Atmung

Veugen CCAFM, Teunissen EM, den Otter LAS, Kos MP, Stokroos RJ, Copper MP.
PMID: 33098537
Sleep Breath. 2021 Sep;25(3):1267-1275. doi: 10.1007/s11325-020-02219-6. Epub 2020 Oct 24.

PURPOSE: To evaluate the performance of the NoSAS (neck, obesity, snoring, age, sex) score, the STOP-Bang (snoring, tiredness, observed apneas, blood pressure, body mass index, age, neck circumference, gender) questionnaire, and the Epworth sleepiness score (ESS) as a screening...

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Veugen CCAFM, Teunissen EM, den Otter LAS, et al. Prediction of obstructive sleep apnea: comparative performance of three screening instruments on the apnea-hypopnea index and the oxygen desaturation index. Sleep Breath. 2020;25(3):1267-1275doi: 10.1007/s11325-020-02219-6.
Veugen, C. C. A. F. M., Teunissen, E. M., den Otter, L. A. S., Kos, M. P., Stokroos, R. J., & Copper, M. P. (2021). Prediction of obstructive sleep apnea: comparative performance of three screening instruments on the apnea-hypopnea index and the oxygen desaturation index. Sleep & breathing = Schlaf & Atmung, 25(3), 1267-1275. https://doi.org/10.1007/s11325-020-02219-6
Veugen, Christianne C A F M, et al. "Prediction of obstructive sleep apnea: comparative performance of three screening instruments on the apnea-hypopnea index and the oxygen desaturation index." Sleep & breathing = Schlaf & Atmung vol. 25,3 (2021): 1267-1275. doi: https://doi.org/10.1007/s11325-020-02219-6
Veugen CCAFM, Teunissen EM, den Otter LAS, Kos MP, Stokroos RJ, Copper MP. Prediction of obstructive sleep apnea: comparative performance of three screening instruments on the apnea-hypopnea index and the oxygen desaturation index. Sleep Breath. 2021 Sep;25(3):1267-1275. doi: 10.1007/s11325-020-02219-6. Epub 2020 Oct 24. PMID: 33098537; PMCID: PMC8376723.
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Geometric approach to the pressure tensor and the elastic constants.

Physical review. E, Statistical, nonlinear, and soft matter physics

den Otter WK, Kröhn M, Clarke JH.
PMID: 11800817
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jan;65(1):016704. doi: 10.1103/PhysRevE.65.016704. Epub 2001 Dec 21.

Expressions are obtained for the pressure tensor in the canonical and the microcanonical ensemble for both isolated and periodic systems, using the same geometric approach to thermodynamic derivatives as has been used previously to define the configurational temperature. The...

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den Otter WK, Kröhn M, Clarke JH. Geometric approach to the pressure tensor and the elastic constants. Phys Rev E Stat Nonlin Soft Matter Phys. 2001;65(1):016704doi: 10.1103/PhysRevE.65.016704.
den Otter, W. K., Kröhn, M., & Clarke, J. H. (2002). Geometric approach to the pressure tensor and the elastic constants. Physical review. E, Statistical, nonlinear, and soft matter physics, 65(1), 016704. https://doi.org/10.1103/PhysRevE.65.016704
den Otter, W K, et al. "Geometric approach to the pressure tensor and the elastic constants." Physical review. E, Statistical, nonlinear, and soft matter physics vol. 65,1 (2002): 016704. doi: https://doi.org/10.1103/PhysRevE.65.016704
den Otter WK, Kröhn M, Clarke JH. Geometric approach to the pressure tensor and the elastic constants. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jan;65(1):016704. doi: 10.1103/PhysRevE.65.016704. Epub 2001 Dec 21. PMID: 11800817.
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Olfactory sensitivities of mosquitoes with different host preferences (Anopheles gambiae s.s., An. arabiensis, An. quadriannulatus, An. m. atroparvus) to synthetic host odours.

Journal of insect physiology

van den Broek IV, den Otter CJ.
PMID: 12770275
J Insect Physiol. 1999 Nov;45(11):1001-1010. doi: 10.1016/s0022-1910(99)00081-5.

Responses of antennal olfactory cells associated with sensilla trichodea were recorded in females of four Anopheles species (Diptera, Culicidae) with different host preferences: the anthropophilic An. gambiae s.s., the opportunistic An. arabiensis, and the zoophilic An. quadriannulatus and An....

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van den Broek IV, den Otter CJ. Olfactory sensitivities of mosquitoes with different host preferences (Anopheles gambiae s.s., An. arabiensis, An. quadriannulatus, An. m. atroparvus) to synthetic host odours. J Insect Physiol. 1999;45(11):1001-1010doi: 10.1016/s0022-1910(99)00081-5.
van den Broek, I. V., & den Otter, C. J. (1999). Olfactory sensitivities of mosquitoes with different host preferences (Anopheles gambiae s.s., An. arabiensis, An. quadriannulatus, An. m. atroparvus) to synthetic host odours. Journal of insect physiology, 45(11), 1001-1010. https://doi.org/10.1016/s0022-1910(99)00081-5
van den Broek, I V.F., and den Otter, C J.. "Olfactory sensitivities of mosquitoes with different host preferences (Anopheles gambiae s.s., An. arabiensis, An. quadriannulatus, An. m. atroparvus) to synthetic host odours." Journal of insect physiology vol. 45,11 (1999): 1001-1010. doi: https://doi.org/10.1016/s0022-1910(99)00081-5
van den Broek IV, den Otter CJ. Olfactory sensitivities of mosquitoes with different host preferences (Anopheles gambiae s.s., An. arabiensis, An. quadriannulatus, An. m. atroparvus) to synthetic host odours. J Insect Physiol. 1999 Nov;45(11):1001-1010. doi: 10.1016/s0022-1910(99)00081-5. PMID: 12770275.
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Microphase separation and liquid-crystalline ordering of rod-coil copolymers.

The Journal of chemical physics

AlSunaidi A, den Otter WK, Clarke JH.
PMID: 19334892
J Chem Phys. 2009 Mar 28;130(12):124910. doi: 10.1063/1.3089701.

Microphase separation and liquid-crystalline ordering in diblock and triblock rod-coil copolymers (with rod-to-coil fraction f=0.5) were investigated using the dissipative particle dynamics method. When the isotropic disordered phases of these systems were cooled down below their order-disorder transition temperatures...

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AlSunaidi A, den Otter WK, Clarke JH. Microphase separation and liquid-crystalline ordering of rod-coil copolymers. J Chem Phys. 2009;130(12):124910doi: 10.1063/1.3089701.
AlSunaidi, A., den Otter, W. K., & Clarke, J. H. (2009). Microphase separation and liquid-crystalline ordering of rod-coil copolymers. The Journal of chemical physics, 130(12), 124910. https://doi.org/10.1063/1.3089701
AlSunaidi, A, et al. "Microphase separation and liquid-crystalline ordering of rod-coil copolymers." The Journal of chemical physics vol. 130,12 (2009): 124910. doi: https://doi.org/10.1063/1.3089701
AlSunaidi A, den Otter WK, Clarke JH. Microphase separation and liquid-crystalline ordering of rod-coil copolymers. J Chem Phys. 2009 Mar 28;130(12):124910. doi: 10.1063/1.3089701. PMID: 19334892.
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"In search of excellence-.

Occupational therapy in health care

Madill HM, Brintnell ES, den Otter R.
PMID: 23944859
Occup Ther Health Care. 1986;3(2):117-27. doi: 10.1080/J003v03n02_10.

Peters and Waterman (1983) have reviewed and profiled some of America's leading corporations, in order to determine what might account for their success. This paper reviews Peters' and Waterman's basic tenets and draws parallels for occupational therapy. The outcome...

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Madill HM, Brintnell ES, den Otter R. "In search of excellence-. Occup Ther Health Care. 1986;3(2):117-27doi: 10.1080/J003v03n02_10.
Madill, H. M., Brintnell, E. S., & den Otter, R. (1986). "In search of excellence-. Occupational therapy in health care, 3(2), 117-27. https://doi.org/10.1080/J003v03n02_10
Madill, H M, et al. ""In search of excellence-." Occupational therapy in health care vol. 3,2 (1986): 117-27. doi: https://doi.org/10.1080/J003v03n02_10
Madill HM, Brintnell ES, den Otter R. "In search of excellence-. Occup Ther Health Care. 1986;3(2):117-27. doi: 10.1080/J003v03n02_10. PMID: 23944859.
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Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations.

The Journal of chemical physics

Tao YG, den Otter WK, Dhont JK, Briels WJ.
PMID: 16613476
J Chem Phys. 2006 Apr 07;124(13):134906. doi: 10.1063/1.2180251.

The isotropic-nematic spinodals of solutions of rigid spherocylindrical colloids with various shape anisotropies L/D in a wide range from 10 to 60 are investigated by means of Brownian dynamics simulations. To make these simulations feasible, we developed a new...

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Tao YG, den Otter WK, Dhont JK, et al. Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations. J Chem Phys. 2006;124(13):134906doi: 10.1063/1.2180251.
Tao, Y. G., den Otter, W. K., Dhont, J. K., & Briels, W. J. (2006). Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations. The Journal of chemical physics, 124(13), 134906. https://doi.org/10.1063/1.2180251
Tao, Yu-Guo, et al. "Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations." The Journal of chemical physics vol. 124,13 (2006): 134906. doi: https://doi.org/10.1063/1.2180251
Tao YG, den Otter WK, Dhont JK, Briels WJ. Isotropic-nematic spinodals of rigid long thin rodlike colloids by event-driven Brownian dynamics simulations. J Chem Phys. 2006 Apr 07;124(13):134906. doi: 10.1063/1.2180251. PMID: 16613476.
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Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods.

The Journal of chemical physics

Tao YG, den Otter WK, Padding JT, Dhont JK, Briels WJ.
PMID: 16035812
J Chem Phys. 2005 Jun 22;122(24):244903. doi: 10.1063/1.1940031.

Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, Oxford, 1986)] and Kuzuu [J. Phys. Soc....

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Tao YG, den Otter WK, Padding JT, et al. Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods. J Chem Phys. 2005;122(24):244903doi: 10.1063/1.1940031.
Tao, Y. G., den Otter, W. K., Padding, J. T., Dhont, J. K., & Briels, W. J. (2005). Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods. The Journal of chemical physics, 122(24), 244903. https://doi.org/10.1063/1.1940031
Tao, Yu-Guo, et al. "Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods." The Journal of chemical physics vol. 122,24 (2005): 244903. doi: https://doi.org/10.1063/1.1940031
Tao YG, den Otter WK, Padding JT, Dhont JK, Briels WJ. Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods. J Chem Phys. 2005 Jun 22;122(24):244903. doi: 10.1063/1.1940031. PMID: 16035812.
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Showing 1 to 12 of 40 entries