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1

Precise global collision detection in multi-axis NC-machining

Oleg Ilushin, Gershon Elber, Dan Halperin, Ron Wein, Myung-Soo Kim

Journal:

Computer-Aided Design

Year:

2005

Language:

english

File:

PDF, 407 KB

english, 2005

2

Stochastic Path Approach to Compute Atomically Detailed Trajectories: Application to the Folding of C Peptide

Elber, Ron, Meller, Jaroslaw, Olender, Roberto

Journal:

Journal of Physical Chemistry B

Year:

1999

Language:

english

File:

PDF, 228 KB

english, 1999

3

Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface

Valentine, Mason L., Cardenas, Alfredo E., Elber, Ron, Baiz, Carlos R.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 1.86 MB

english, 2018

4

On the design and analysis of protein folding potentials

Dror Tobi, Gil Shafran, Nathan Linial, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 157 KB

english, 2000

5

Revisiting and parallelizing SHAKE

Yael Weinbach, Ron Elber

Journal:

Journal of Computational Physics

Year:

2005

Language:

english

File:

PDF, 198 KB

english, 2005

6

SSALN: An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs

Jian Qiu, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 532 KB

english, 2006

7

Large-scale linear programming techniques for the design of protein folding potentials

Michael Wagner, Jarosław Meller, Ron Elber

Journal:

Mathematical Programming

Year:

2004

Language:

english

File:

PDF, 166 KB

english, 2004

8

Computational study of peptide permeation through membrane: searching for hidden slow variables

Cardenas, Alfredo E., Elber, Ron

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

9

New simulation methods for proteins and DNA

Journal:

Current Opinion in Structural Biology

Year:

1993

Language:

english

File:

PDF, 534 KB

english, 1993

10

Calculation of classical trajectories with a very large time step: Formalism and numerical examples

Olender, Roberto, Elber, Ron

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 637 KB

english, 1996

11

A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces

Di Pierro, Michele, Elber, Ron, Leimkuhler, Benedict

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

12

[WORLD SCIENTIFIC Proceedings of the International School of Physics - LERICI, Villa Marigola (7 – 18 July 1997)] Classical and Quantum Dynamics in Condensed Phase Simulations - Dynamics of peptide folding

ELBER, RON, MOHANTY, DEBASISA, SIMMERLING, CARLOS

Language:

english

File:

PDF, 1.87 MB

english

13

Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization

Viswanath, Shruthi, Dominguez, Laura, Foster, Leigh S., Straub, John E., Elber, Ron

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 843 KB

english, 2015

14

A new paradigm for atomically detailed simulations of kinetics in biophysical systems

Journal:

Quarterly Reviews of Biophysics

Year:

2017

Language:

english

File:

PDF, 724 KB

english, 2017

15

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

Templeton, Clark, Chen, Szu-Hua, Fathizadeh, Arman, Elber, Ron

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 25.87 MB

english, 2017

16

Risk for Low Pathogenicity Avian Influenza Virus on Poultry Farms, the Netherlands, 2007–2013

Bouwstra, Ruth, Gonzales, Jose L., de Wit, Sjaak, Stahl, Julia, Fouchier, Ron A.M., Elbers, Armin R.W.

Journal:

Emerging Infectious Diseases

Year:

2017

Language:

english

File:

PDF, 625 KB

english, 2017

17

Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations

Chen, Yen-Lin, Lee, Tongsik, Elber, Ron, Pollack, Lois

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 2.36 MB

english, 2019

18

Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics

Journal:

Annual Review of Biophysics

Year:

2020

File:

PDF, 2.60 MB

2020

19

Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories

Klara Kedem, L. Paul Chew, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 921 KB

english, 1999

20

Distance-dependent, pair potential for protein folding: Results from linear optimization

Dror Tobi, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 122 KB

english, 2000

21

The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study

Dror Tobi, Ron Elber, Devarajan Thirumalai

Journal:

Year:

2003

Language:

english

File:

PDF, 244 KB

english, 2003

22

Early Structural Evolution of Native Cytochrome c after Solvent Removal

Michal Z. Steinberg, Ron Elber, Fred W. McLafferty, R. Benny Gerber, Kathrin Breuker

Journal:

Year:

2008

Language:

english

File:

PDF, 646 KB

english, 2008

23

ChemInform Abstract: Long Time Dynamics of Complex Systems

Ron Elber, Avijit Ghosh, Alfredo Cardenas

Journal:

Year:

2002

File:

PDF, 24 KB

2002

24

Maximum feasibility guideline in the design and analysis of protein folding potentials

Jaroslaw Meller, Michael Wagner, Ron Elber

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 145 KB

english, 2002

25

Calculations of a list of neighbors in Molecular Dynamics simulations

Virginia Yip, Ron Elber

Journal:

Journal of Computational Chemistry

Year:

1989

Language:

english

File:

PDF, 650 KB

english, 1989

26

Dissociation dynamics in high-energy molecule—surface collisions: The dissociation rainbow effect

Ron Elber, R.B. Gerber

Journal:

Chemical Physics Letters

Year:

1983

Language:

english

File:

PDF, 412 KB

english, 1983

27

Vibrational and rotational excitation in high-energy molecule-surface collisions: Dominance of the rotational mode

R.B. Gerber, Ron Elber

Journal:

Chemical Physics Letters

Year:

1983

Language:

english

File:

PDF, 526 KB

english, 1983

28

Excitation of molecular rotation and of solid vibrations in high-energy collisions of I2 with MgO(100)

Ron Elber, R.B. Gerber

Journal:

Chemical Physics Letters

Year:

1985

Language:

english

File:

PDF, 481 KB

english, 1985

29

MOIL: A program for simulations of macromolecules

Ron Elber, Adrian Roitberg, Carlos Simmerling, Robert Goldstein, Haiying Li, Gennady Verkhivker, Chen Keasar, Jing Zhang, Alex Ulitsky

Journal:

Computer Physics Communications

Year:

1995

Language:

english

File:

PDF, 2.28 MB

english, 1995

30

Parallel computations of molecular dynamics trajectories using the stochastic path approach

Veaceslav Zaloj, Ron Elber

Journal:

Computer Physics Communications

Year:

2000

Language:

english

File:

PDF, 150 KB

english, 2000

31

Ion permeation through the gramicidin channel: Atomically detailed modeling by the stochastic difference equation

Koneshan Siva, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 432 KB

english, 2003

32

Kinetics of cytochrome C folding: Atomically detailed simulations

Alfredo E. Cárdenas, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 250 KB

english, 2003

33

Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase

Joost C.M. Uitdehaag, Bart A. van der Veen, Lubbert Dijkhuizen, Ron Elber, Bauke W. Dijkstra

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 407 KB

english, 2001

34

Enriching the sequence substitution matrix by structural information

Octavian Teodorescu, Tamara Galor, Jaroslaw Pillardy, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 129 KB

english, 2004

35

Linear programming optimization and a double statistical filter for protein threading protocols

Jaroslaw Meller, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 333 KB

english, 2001

36

Atomically detailed potentials to recognize native and approximate protein structures

Jian Qiu, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 412 KB

english, 2005

37

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

Brinda Kizhakke Vallat, Jaroslaw Pillardy, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 697 KB

english, 2008

38

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

Peter Májek, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 623 KB

english, 2009

39

Building and assessing atomic models of proteins from structural templates: Learning and benchmarks

Brinda Kizhakke Vallat, Jaroslaw Pillardy, Peter Májek, Jaroslaw Meller, Thomas Blom, BaoQiang Cao, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 324 KB

english, 2009

40

PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking

D. V. S. Ravikant, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 894 KB

english, 2010

41

Computational exploration of the network of sequence flow between protein structures

Baoqiang Cao, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 637 KB

english, 2010

42

Super folds, networks, and barriers

Sean Burke, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 573 KB

english, 2012

43

Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin

Danuta Rojewska, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1990

Language:

english

File:

PDF, 1.13 MB

english, 1990

44

Computational studies of ligand diffusion in globins: I. Leghemoglobin

Ryszard Czerminski, Dr. Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1991

Language:

english

File:

PDF, 985 KB

english, 1991

45

Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems

Ryszard Czerminski, Ron Elber

Journal:

International Journal of Quantum Chemistry

Year:

1990

Language:

english

File:

PDF, 915 KB

english, 1990

46

Computer simulations of protein folding: Classical trajectories by optimization of action

Journal:

Computer Physics Communications

Year:

2005

Language:

english

File:

PDF, 329 KB

english, 2005

47

Unassisted Transport of N-Acetyl-l-tryptophanamide through Membrane: Experiment and Simulation of Kinetics

Cardenas, Alfredo E., Jas, Gouri S., DeLeon, Kristine Y., Hegefeld, Wendy A., Kuczera, Krzysztof, Elber, Ron

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 5.75 MB

english, 2012

48

[Lecture Notes in Computational Science and Engineering] New Algorithms for Macromolecular Simulation Volume 49 || Free Energy Calculations in Biological Systems. How Useful Are They in Practice?

Leimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christoph, Skeel, Robert

Year:

2006

Language:

english

File:

PDF, 556 KB

english, 2006

49

Long-timescale simulation methods

Journal:

Current Opinion in Structural Biology

Year:

2005

Language:

english

File:

PDF, 124 KB

english, 2005

50

Ligand diffusion in globins: simulations versus experiment

Journal:

Current Opinion in Structural Biology

Year:

2010

Language:

english

File:

PDF, 200 KB

english, 2010

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