Sodt, Alexander J.: search on Z-Library

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1

Bending Free Energy from Simulation: Correspondence of Planar and Inverse Hexagonal Lipid Phases

Sodt, Alexander J., Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 1.49 MB

english, 2013

2

The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length

Perrin, Bradley S., Sodt, Alexander J., Cotten, Myriam L., Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 37 KB

english, 2015

3

Cholesterol-Dependent Bending Energies in Both Leaves Play a Significant Role in Determining the Cholesterol Distribution in the Plasma Membrane

Allender, David, Sodt, Alexander J., Schick, Michael

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 44 KB

2019

4

All-Atom Molecular Dynamics Simulations of Ganglioside GM1 and its Degradation Products

Beaven, Andrew H., Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 40 KB

2020

5

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

Venable, Richard M., Sodt, Alexander J., Rogaski, Brent, Rui, Huan, Hatcher, Elizabeth, MacKerell, Alexander D., Pastor, Richard W., Klauda, Jeffery B.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

6

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

Sodt, Alexander J., Mei, Ye, König, Gerhard, Tao, Peng, Steele, Ryan P., Brooks, Bernard R., Shao, Yihan

Journal:

Journal of Physical Chemistry A

Year:

2015

Language:

english

File:

PDF, 2.12 MB

english, 2015

7

The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length

Perrin, B. Scott, Sodt, Alexander J., Cotten, Myriam L., Pastor, Richard W.

Journal:

Journal of Membrane Biology

Year:

2015

Language:

english

File:

PDF, 1.97 MB

english, 2015

8

Nanoscale Structure of Lipid Bilayers Revealed By In-Silico and Experimental Small Angle Neutron Scattering

Dorrell, Mitchell, Heberle, Fred, Katsaras, John, Lyman, Ed, Sodt, Alexander

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 48 KB

english, 2018

9

Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: Microsecond molecular dynamics simulations of ErbB1/B2 and EphA1

Zhang, Liqun, Sodt, Alexander J., Venable, Richard M., Pastor, Richard W., Buck, Matthias

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 862 KB

english, 2013

10

The tension of a curved surface from simulation

Sodt, Alexander J., Pastor, Richard W.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.25 MB

english, 2012

11

Exploring Apparent Membrane Stiffness due to the Presence of GM1 using a Continuum Model

Sapp, Kayla, Sodt, Alexander

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 43 KB

english, 2018

12

Laterally Resolved Small-Angle Scattering Intensity from Lipid Bilayer Simulations: An Exact and a Limited-Range Treatment

Dorrell, Mitchell W., Heberle, Frederick A., Katsaras, John, Maibaum, Lutz, Lyman, Edward, Sodt, Alexander J.

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 6.06 MB

2020

13

Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation

Beaven, Andrew H., Maer, Andreia M., Sodt, Alexander J., Rui, Huan, Pastor, Richard W., Andersen, Olaf S., Im, Wonpil

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

14

Protocol and Validation of CHARMM-GUI Hex Phase Builder

Beaven, Andrew H., Sodt, Alexander J., Pastor, Richard W., Im, Wonpil

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 58 KB

english, 2017

15

Nanoscale Structure of Lipid Bilayers Revealed by In-Silico and Experimental Small Angle Neutron Scattering

Dorrell, Mitchell, Heberle, Frederick A., Katsaras, John, Lyman, Edward, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 50 KB

english, 2019

16

Partially Automated Identification of Curvature-Sensitive Collective Lipid Structure

Beaven, Andrew H., Sapp, Kayla, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 66 KB

2020

17

Nanoscale Structure and Dynamics of the Liquid Ordered Phase

Alexander, Sodt J., Gawrisch, Klaus, Pastor, Richard W., Lyman, Edward R.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

18

Hemagglutinin Palmitoylation Contributes to Membrane Curvature in Influenza a Virus Assembly and Membrane Fusion

Chlanda, Petr, Mekhedov, Elena, Waters, Hang, Sodt, Alexander, Blank, Paul S., Zimmerberg, Joshua

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 45 KB

english, 2017

19

Molecular Simulation and Continuum Modeling of N-Bar-Induced Lipid Membrane Deformations

Beaven, Andrew H., Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 41 KB

english, 2019

20

Depth of α-Synuclein in a Bilayer Determined by Fluorescence, Neutron Reflectometry, and Computation

Pfefferkorn, Candace M., Heinrich, Frank, Sodt, Alexander J., Maltsev, Alexander S., Pastor, Richard W., Lee, Jennifer C.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 783 KB

english, 2012

21

Quantitative Molecular Modeling of Membrane Curvature Induction by an Amphipathic Helix

Sodt, Alexander J., Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

22

Lipid-Lipid Coupling to Membrane Curvature by Simulation and NMR

Sodt, Alexander J., Soubias, Olivier, Gawrisch, Klaus, Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

23

Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model

Sodt, Alexander J., Beaven, Andrew H., Andersen, Olaf S., Im, Wonpil, Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 1.23 MB

english, 2017

24

Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin

Sodt, Alexander J., Pastor, Richard W., Lyman, Edward

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

25

All-Atom Simulation and Continuum Elastic Theory of Gramicidin a in Binary Component Lipid Bilayers

Beaven, Andrew H., Sodt, Alexander J., Greathouse, Denise V., Koeppe, Roger E., Pastor, Richard W., Andersen, Olaf S., Im, Wonpil

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 44 KB

english, 2014

26

Molecular Dynamics Prediction and Refinement of Transmembrane Helix Dimers

Zhang, Liqun, Sodt, Alexander, Venable, Rick, Pastor, Richard W., Buck, Matthias

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 51 KB

english, 2012

27

Controlling GPCR Rhodopsin Function by Small, Physiologically Relevant Changes in Bilayer Hydrophobic Thickness

Soubias, Olivier, Sodt, Alexander J., Teague, Walter E., Hines, Kirk G., Gawrisch, Klaus

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 39 KB

english, 2016

28

Cation-Selective Channel Regulated by Anions According to Their Hofmeister Ranking

Gurnev, Philip A., Roark, Torri C., Petrache, Horia I., Sodt, Alexander J., Bezrukov, Sergey M.

Journal:

Angewandte Chemie International Edition

Year:

2017

Language:

english

File:

PDF, 1.45 MB

english, 2017

29

Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes

Beaven, Andrew H, Sodt, Alexander J., Pastor, Richard Walter, Koeppe, Roger E., Andersen, Olaf S., Im, Wonpil

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.86 MB

english, 2017

30

Building Blocks of the Outer Membrane: Calculating a general elastic energy model for β-barrel membrane proteins

Lessen, Henry J., Fleming, Patrick J., Fleming, Karen Gibson, Sodt, Alexander J.

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 2.06 MB

english, 2018

31

Continuum-Modeling Software for Modeling the Dynamics of Arbitrary Topology Membranes

Sapp, Kayla, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

32

Cholesterol-Dependent Bending Energies in Both Leaves Play a Significant Role in Determining the Cholesterol Distribution in the Plasma Membrane

Allender, David, Sodt, Alexander J., Schick, Michael

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 44 KB

english, 2019

33

New and Notable: Differential or curvature stress? Modus vivendi

Lyman, Edward, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 239 KB

english, 2019

34

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

Sodt, Alexander J., Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 760 KB

english, 2014

35

Amphipathic Helices—Wedge? Or Nae Nae?

Lyman, Edward, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 79 KB

english, 2016

36

Cation-Selective Channel Regulated by Anions According to Their Hofmeister Ranking

Gurnev, Philip A., Roark, Torri C., Petrache, Horia I., Sodt, Alexander J., Bezrukov, Sergey M.

Journal:

Angewandte Chemie

Year:

2017

Language:

english

File:

PDF, 1.47 MB

english, 2017

37

New and Notable: Differential or curvature stress? Modus vivendi

Lyman, Edward, Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 239 KB

2019

38

Lipid Chain Entropy and Exchange in the Vicinity of G-Protein Coupled Receptors

Leonard, Alison, Sodt, Alexander J., Lyman, Edward R.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 45 KB

2020

39

A combined molecular/continuum-modeling approach to predict the small-angle neutron scattering of curved membranes

Dorrell, Mitchell W., Beaven, Andrew H., Sodt, Alexander J.

Journal:

Chemistry and Physics of Lipids

Year:

2020

File:

PDF, 388 KB

2020

40

Investigating MUC1 Transmembrane Dimer Structure using Replica Exchange Molecular Dynamics

Freeman, Christina M., Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

41

Modeling Relaxation Timescales of Coupled Membrane/Protein Systems

Sapp, Kayla, Sodt, Alexander J., Maibaum, Lutz

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 43 KB

english, 2019

42

The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers

Sodt, Alexander J., Sandar, Michael Logan, Gawrisch, Klaus, Pastor, Richard W., Lyman, Edward

Journal:

Journal of the American Chemical Society

Year:

2014

Language:

english

File:

PDF, 479 KB

english, 2014

43

Computationally Determined Free Energy Profiles of the Mucin-1 Transmembrane Homodimer

Freeman, Christina M., Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2018

File:

PDF, 39 KB

2018

44

Effect of Lipid Structure and Material Properties on the Membrane Stability to Pore Formation

Galimzyanov, Timur R., Beaven, Andrew H., Kalutskiy, Maxim A., Sodt, Alexander J., Blank, Paul S., Zimmerberg, Joshua, Akimov, Sergey A., Batishchev, Oleg V.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 39 KB

2020

45

Lipid Bilayer Curvature Frustration

Sodt, Alexander J., Pastor, Richard W.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

46

Palmitoylation contributes to membrane curvature in Influenza A virus assembly and hemagglutinin-mediated membrane fusion

Chlanda, Petr, Mekhedov, Elena, Waters, Hang, Sodt, Alexander, Schwartz, Cindi, Nair, Vinod, Blank, Paul S., Zimmerberg, Joshua

Journal:

Journal of Virology

Year:

2017

Language:

english

File:

PDF, 8.86 MB

english, 2017

47

Molecular Simulation and Continuum Modeling of N-Bar-Induced Lipid Membrane Deformations

Beaven, Andrew H., Sodt, Alexander J.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 41 KB

2019

48

An Implicit Lipid Model for Efficient Reaction Diffusion Simulations of Proteins Binding to Arbitrary Surfaces

Fu, Yiben, Sodt, Alexander J., Johnson, Margaret E.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

49

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

Tao, Peng, Sodt, Alexander J., Shao, Yihan, König, Gerhard, Brooks, Bernard R.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.60 MB

english, 2014

50

Ion Channel Regulation by Lipid Bilayers: Theory & Simulation of Deformed Membranes around Gramicidin A

Beaven, Andrew H., Sodt, Alexander J., Andersen, Olaf S., Pastor, Richard W., Im, Wonpil

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

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