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1

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Abraham, Mark James, Murtola, Teemu, Schulz, Roland, Páll, Szilárd, Smith, Jeremy C., Hess, Berk, Lindahl, Erik

Journal:

Year:

2015

Language:

english

File:

PDF, 872 KB

english, 2015

2

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Hess, Berk, Kutzner, Carsten, van der Spoel, David, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 383 KB

english, 2008

3

GROMACS: Fast, flexible, and free

David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 338 KB

english, 2005

4

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Erik Lindahl, Berk Hess, David van der Spoel

Journal:

Journal of Molecular Modeling

Year:

2001

Language:

english

File:

PDF, 109 KB

english, 2001

5

LINCS: A linear constraint solver for molecular simulations

Hess, Berk, Bekker, Henk, Berendsen, Herman J. C., Fraaije, Johannes G. E. M.

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 174 KB

english, 1997

6

A flexible algorithm for calculating pair interactions on SIMD architectures

Páll, Szilárd, Hess, Berk

Journal:

Computer Physics Communications

Year:

2013

Language:

english

File:

PDF, 766 KB

english, 2013

7

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties

Wennberg, Christian L., Murtola, Teemu, Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.93 MB

english, 2013

8

Direct-Space Corrections Enable Fast Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation

Wennberg, Christian L, Murtola, Teemu, Pall, Szilard, Abraham, Mark J., Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 355 KB

english, 2015

9

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

Bjelkmar, Pär, Larsson, Per, Cuendet, Michel A., Hess, Berk, Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 203 KB

english, 2010

10

Riemann metric approach to optimal sampling of multidimensional free-energy landscapes

Lindahl, Viveca, Lidmar, Jack, Hess, Berk

Journal:

Physical Review E

Year:

2018

Language:

english

File:

PDF, 657 KB

english, 2018

11

Water–substrate physico-chemistry in wetting dynamics

Johansson, Petter, Carlson, Andreas, Hess, Berk

Journal:

Journal of Fluid Mechanics

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

12

Sequence dependency of canonical base pair opening in the DNA double helix

Lindahl, Viveca, Villa, Alessandra, Hess, Berk, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 6.74 MB

english, 2017

13

GROMACS—the road ahead

David van der Spoel, Berk Hess

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 123 KB

english, 2011

14

Flexible constraints: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water

Hess, Berk, Saint-Martin, Humberto, Berendsen, Herman J. C.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 388 KB

english, 2002

15

Modeling Multibody Effects in Ionic Solutions with a Concentration Dependent Dielectric Permittivity

Hess, Berk, Holm, Christian, van der Vegt, Nico

Journal:

Physical Review Letters

Year:

2006

Language:

english

File:

PDF, 195 KB

english, 2006

16

Interaction of Water with N,N′−1,2-Ethanediyl-bis(6-hydroxy-hexanamide) Crystals: A Simulation Study

Hess, Berk, Harings, Jules A. W., Rastogi, Sanjay, Vegt, Nico F. A. van der

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 369 KB

english, 2009

17

An application of flexible constraints in Monte Carlo simulations of the isobaric–isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model

Saint-Martin, Humberto, Hess, Berk, Berendsen, Herman J. C.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 472 KB

english, 2004

18

Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate

Hess, Berk, Le?n, Salvador, van der Vegt, Nico, Kremer, Kurt

Journal:

Year:

2006

Language:

english

File:

PDF, 380 KB

english, 2006

19

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

Lindahl, Viveca, Gourdon, Pontus, Andersson, Magnus, Hess, Berk

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.92 MB

english, 2018

20

Effects of omega-3 PUFA on the vitamin E and glutathione antioxidant defense system in individuals at ultra-high risk of psychosis

Smesny, Stefan, Milleit, Berko, Schaefer, Miriam R., Hipler, Uta-Christina, Milleit, Christine, Wiegand, Cornelia, Hesse, Jana, Klier, Claudia M., Holub, Magdalena, Holzer, Ingrid, Berk, Michael, McGo

Journal:

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA)

Year:

2015

Language:

english

File:

PDF, 551 KB

english, 2015

21

Phase IB Study of the mTOR Inhibitor Ridaforolimus With Capecitabine

Perotti, A., Locatelli, A., Sessa, C., Hess, D., Vigano, L., Capri, G., Maur, M., Cerny, T., Cresta, S., Rojo, F., Albanell, J., Marsoni, S., Corradino, I., Berk, L., Rivera, V. M., Haluska, F., Giann

Journal:

Journal of Clinical Oncology

Year:

2010

Language:

english

File:

PDF, 275 KB

english, 2010

22

310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State

Schwaiger, Christine S., Bjelkmar, Pär, Hess, Berk, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

23

Modeling Solubilities of Additives in Polymer Microstructures: Single-Step Perturbation Method Based on a Soft-Cavity Reference State

Özal, Tugba A., Peter, Christine, Hess, Berk, van der Vegt, Nico F. A.

Journal:

Year:

2008

Language:

english

File:

PDF, 700 KB

english, 2008

24

Phe233 in the Voltage-Sensor is Rate Limiting for Channel Closure but not for the Opening

Schwaiger, Christine S., Börjesson, Sara I., Hess, Berk, Elinder, Fredrik, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

25

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions

Kasson, Peter M., Hess, Berk, Lindahl, Erik

Journal:

Chemistry and Physics of Lipids

Year:

2013

Language:

english

File:

PDF, 931 KB

english, 2013

26

The Free Energy Barrier for Arginine Gating Charge Translation Is Altered by Mutations in the Voltage Sensor Domain

Schwaiger, Christine S., Börjesson, Sara I., Hess, Berk, Wallner, Björn, Elinder, Fredrik, Lindahl, Erik, Attali, Bernard

Journal:

Year:

2012

Language:

english

File:

PDF, 1.70 MB

english, 2012

27

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems

Feenstra, K. Anton, Hess, Berk, Berendsen, Herman J. C.

Journal:

Journal of Computational Chemistry

Year:

1999

Language:

english

File:

PDF, 231 KB

english, 1999

28

Similarities between principal components of protein dynamics and random diffusion

Journal:

Physical Review E

Year:

2000

Language:

english

File:

PDF, 265 KB

english, 2000

29

Stability of Hydrophobically Modified Poly( p -phenylenesulfonate) Bundles As Observed by Molecular Dynamics Simulation

Hess, Berk, Sayar, Mehmet, Holm, Christian

Journal:

Year:

2007

Language:

english

File:

PDF, 188 KB

english, 2007

30

Reproducible Polypeptide Folding and Structure Prediction using Molecular Dynamics Simulations

M. Marvin Seibert, Alexandra Patriksson, Berk Hess, David van der Spoel

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 756 KB

english, 2005

31

Osmotic coefficients of atomistic NaCl (aq) force fields

Hess, Berk, Holm, Christian, van der Vegt, Nico

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 520 KB

english, 2006

32

Competing Adsorption between Hydrated Peptides and Water onto Metal Surfaces: From Electronic to Conformational Properties

Ghiringhelli, Luca M., Hess, Berk, van der Vegt, Nico F. A., Delle Site, Luigi

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 786 KB

english, 2008

33

Predictive Modeling of Phenol Chemical Potentials in Molten Bisphenol A−Polycarbonate over a Broad Temperature Range

Hess, Berk, van der Vegt, Nico F. A.

Journal:

Year:

2008

Language:

english

File:

PDF, 64 KB

english, 2008

34

Fast-Growth Thermodynamic Integration: Calculating Excess Chemical Potentials of Additive Molecules in Polymer Microstructures

Hess, Berk, Peter, Christine, Ozal, Tugba, van der Vegt, Nico F. A.

Journal:

Year:

2008

Language:

english

File:

PDF, 146 KB

english, 2008

35

Steady moving contact line of water over a no-slip substrate

LÄcis, UÇ§is, Johansson, Petter, Fullana, Tomas, Hess, Berk, Amberg, Gustav, Bagheri, Shervin, Zaleski, StephanÃ©

Journal:

The European Physical Journal Special Topics

Year:

2020

File:

PDF, 1.75 MB

2020

36

Determining the shear viscosity of model liquids from molecular dynamics simulations

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 406 KB

english, 2002

37

Antiviral effect of prolonged intermittent lymphoblastoid alpha interferon treatment in chronic hepatitis B.

Janssen, H L, Berk, L, Schalm, S W, Heijtink, R A, Hess, G, Rossol, S, Meyer zum Buschenfelde, K H, Chamuleau, R A, Jansen, P L, Reesink, H W

Journal:

Year:

1992

Language:

english

File:

PDF, 914 KB

english, 1992

38

Gromex: Electrostatics with Chemical Variability for Realistic Molecular Simulations on the Exascale

Ullmann, R. Thomas, Kutzner, Carsten, Beckmann, Andreas, Kohnke, Bartosz, Haensel, David, Kabadshow, Ivo, Dachsel, Holger, Hess, Berk, Grubmüller, Helmut

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 65 KB

english, 2017

39

Convergence of sampling in protein simulations

Journal:

Physical Review E

Year:

2002

Language:

english

File:

PDF, 410 KB

english, 2002

40

Analysis and Evaluation of Channel Models: Simulations of Alamethicin

Peter Tieleman, D., Hess, Berk, Sansom, Mark S.P.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 2.84 MB

english, 2002

41

Molecular dynamics study of dislocation nucleation from a crack tip

Hess, Berk, Thijsse, Barend J., Van der Giessen, Erik

Journal:

Physical Review B

Year:

2005

Language:

english

File:

PDF, 1.53 MB

english, 2005

42

[ACM Press 2011 International Conference for High Performance Computing, Networking, Storage and Analysis - Seattle, Washington (2011.11.12-2011.11.18)] Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '11 - Copernicus

Pronk, Sander, Lindahl, Erik, Larsson, Per, Pouya, Iman, Bowman, Gregory R., Haque, Imran S., Beauchamp, Kyle, Hess, Berk, Pande, Vijay S., Kasson, Peter M.

Year:

2011

Language:

english

File:

PDF, 1.68 MB

english, 2011

43

Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models

Hess, Berk, van der Vegt, Nico F. A.

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 242 KB

english, 2006

44

Local comprehensive plan quality and regional ecosystem protection: The case of the Jordan Lake watershed, North Carolina, U.S.A.

Philip Berke, Danielle Spurlock, George Hess, Larry Band

Journal:

Land Use Policy

Year:

2013

Language:

english

File:

PDF, 490 KB

english, 2013

45

A Flexible, GPU - Powered Fast Multipole Method for Realistic Biomolecular Simulations in Gromacs

Kohnke, Bartosz, Ullmann, R. Thomas, Kutzner, Carsten, Beckmann, Andreas, Haensel, David, Kabadshow, Ivo, Dachsel, Holger, Hess, Berk, Grubmüller, Helmut

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

46

Structural Transition from Alpha- to 3_10-Helix Reduces the Free Energy Required for S4 Translation in Kv1.2/2.1 Voltage Sensors, and F233 Appears to Responsible for the Gating Barrier

Schwaiger, Christine S., Bjelkmar, Pär, Hess, Berk, Lindahl, Erik

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

47

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

PÃ¡ll, SzilÃ¡rd, Zhmurov, Artem, Bauer, Paul, Abraham, Mark, Lundborg, Magnus, Gray, Alan, Hess, Berk, Lindahl, Erik

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 1.61 MB

2020

48

[ACM Press the 2011 companion - Seattle, Washington, USA (2011.11.12-2011.11.18)] Proceedings of the 2011 companion on High Performance Computing Networking, Storage and Analysis Companion - SC '11 Companion - Poster

Páll, Szilárd, Hess, Berk, Lindahl, Erik

Year:

2011

Language:

english

File:

PDF, 285 KB

english, 2011

49

Dynamics and Structure of Ln(III)−Aqua Ions: A Comparative Molecular Dynamics Study Using ab Initio Based Flexible and Polarizable Model Potentials

Villa, Alessandra, Hess, Berk, Saint-Martin, Humberto

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 2.42 MB

english, 2009

50

Solvent-averaged potentials for alkali-, earth alkali-, and alkylammonium halide aqueous solutions

Hess, Berk, van der Vegt, Nico F. A.

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 141 KB

english, 2007

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