Search Results - "Berendsen, H H"

Efficient Algorithms for Langevin and DPD Dynamics by Goga, N, Rzepiela, A. J, de Vries, A. H, Marrink, S. J, Berendsen, H. J. C

“…In this article, we present several algorithms for stochastic dynamics, including Langevin dynamics and different variants of Dissipative Particle Dynamics…”
Get full text

Benchmark of Schemes for Multiscale Molecular Dynamics Simulations by Goga, N, Melo, M. N, Rzepiela, A. J, de Vries, A. H, Hadar, A, Marrink, S. J, Berendsen, H. J. C

“…In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several…”
Get full text

Collective protein dynamics in relation to function by Berendsen, Herman JC, Hayward, Steven

“…Several techniques for the analysis of the internal motions of proteins are available — separating large collective motions from small, presumably…”
Get full text

Stochastic Dynamics with Correct Sampling for Constrained Systems by Peters, E. A. J. F, Goga, N, Berendsen, H. J. C

“…In this paper we discuss thermostatting using stochastic methods for molecular simulations where constraints are present. For so-called impulsive thermostats,…”
Get full text

Data-driven directions for effective footwear provision for the high-risk diabetic foot by Arts, M. L. J., de Haart, M., Waaijman, R., Dahmen, R., Berendsen, H., Nollet, F., Bus, S. A.

“…Aims Custom‐made footwear is used to offload the diabetic foot to prevent plantar foot ulcers. This prospective study evaluates the offloading effects of…”
Get full text

Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes:  Micellar Structure and Chain Relaxation by Tieleman, D. P, van der Spoel, D, Berendsen, H. J. C

“…We simulated micelles of 40 (M40), 54 (M54), and 65 (M65) dodecylphosphocholine (DPC) lipids in water for up to 15 ns and analyzed the system energetics,…”
Get full text

Trehalose: a review of properties, history of use and human tolerance, and results of multiple safety studies by Richards, A.B, Krakowka, S, Dexter, L.B, Schmid, H, Wolterbeek, A.P.M, Waalkens-Berendsen, D.H, Shigoyuki, A, Kurimoto, M

“…This paper contains a review of the history, natural occurrence, human consumption, metabolism, manufacture, and the results of eight standardized animal…”
Get full text

The role of serotonin in hot flushes by Berendsen, Hemmie H.G

“…Hot flushes are experienced in those periods of the female life when estrogen levels are low. Hormone replacement therapy is thus the first choice for…”
Get full text

GROMACS: A message-passing parallel molecular dynamics implementation by Berendsen, H.J.C., van der Spoel, D., van Drunen, R.

“…A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The…”
Get full text

A Molecular Dynamics Study of the Pores Formed by Escherichia coli OmpF Porin in a Fully Hydrated Palmitoyloleoylphosphatidylcholine Bilayer by Tieleman, D.P., Berendsen, H.J.C.

“…In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318…”
Get full text

Voltage-Dependent Insertion of Alamethicin at Phospholipid/Water and Octane/Water Interfaces by Tieleman, D.P., Berendsen, H.J.C., Sansom, M.S.P.

“…Understanding the binding and insertion of peptides in lipid bilayers is a prerequisite for understanding phenomena such as antimicrobial activity and…”
Get full text

The use of GIS in reconstructing the Holocene palaeogeography of the Rhine-Meuse delta, The Netherlands by Berendsen, H. J. A., Cohen, K. M., Stouthamer, E.

“…In Holocene palaeogeographical studies, GIS nowadays is used in various ways, embracing either GIS modelling possibilities or GIS spatial data storage…”
Get full text

5-HT2C receptor agonists: pharmacological characteristics and therapeutic potential by Martin, J R, Bös, M, Jenck, F, Moreau, J, Mutel, V, Sleight, A J, Wichmann, J, Andrews, J S, Berendsen, H H, Broekkamp, C L, Ruigt, G S, Köhler, C, Delft, A M

“…In vitro, (S)-2-(chloro-5-fluoro-indol-1-yl)-1-methylethylamine 1:1 C4H4O4 and (S)-2-(4,4,7-trimethyl-1,4-dihydro-indeno[1, 2-b]pyrrol-1-yl)-1-methylethylamine…”
Get more information

Essential dynamics of proteins by Amadei, A, Linssen, A B, Berendsen, H J

“…Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the…”
Get more information

Premature ejaculation and serotonergic antidepressants-induced delayed ejaculation: the involvement of the serotonergic system by Waldinger, Marcel D, Berendsen, Hemmie H.G, Blok, Bertil F.M, Olivier, Berend, Holstege, Gert

“…Premature ejaculation has generally been considered a psychosexual disorder with psychogenic aetiology. Although still mainly treated by behavioural therapy,…”
Get full text

Developmental immunotoxicity in male rats after juvenile exposure to di- n-octyltin dichloride (DOTC) by Tonk, Elisa C.M., Verhoef, Aart, de la Fonteyne, Liset J.J., Waalkens-Berendsen, Ine D.H., Wolterbeek, André P.M., van Loveren, Henk, Piersma, Aldert H.

“…► The utility of immune assays needs to be evaluated for assessing developmental immunotoxicity. ► TDAR parameters are appropriate for inclusion in…”
Get full text

Developmental immunotoxicity of di-n-octyltin dichloride (DOTC) in an extended one-generation reproductive toxicity study by Tonk, Elisa C.M., de Groot, Didima M.G., Penninks, André H., Waalkens-Berendsen, Ine D.H., Wolterbeek, André P.M., Piersma, Aldert H., van Loveren, Henk

“…► Further evaluation of immune assays is needed to determine their utility in assessing developmental immunotoxicity. ► Splenocyte subpopulation parameters are…”
Get full text

The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water by van Aalten, D M, Amadei, A, Linssen, A B, Eijsink, V G, Vriend, G, Berendsen, H J

“…Comparisons of the crystal structures of thermolysin and the thermolysin-like protease produced by B. cereus have recently led to the hypothesis that neutral…”
Get more information

Prediction of protein conformational freedom from distance constraints by de Groot, B.L., van Aalten, D.M.F., Scheek, R.M., Amadei, A., Vriend, G., Berendsen, H.J.C.

“…A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on…”
Get full text

Developmental immunotoxicity of ethanol in an extended one-generation reproductive toxicity study by Tonk, Elisa C. M., de Groot, Didima M. G., Wolterbeek, André P. M., Penninks, André H., Waalkens-Berendsen, Ine D. H., Piersma, Aldert H., van Loveren, Henk

“…The susceptibility of developing immune system to chemical disruption warrants the assessment of immune parameters in reproductive and developmental testing…”
Get full text