Aksimentiev, A.: search on Z-Library

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1

Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis

Tian, Kai, Decker, Karl, Aksimentiev, Aleksei, Gu, Li-Qun

Journal:

Year:

2017

Language:

english

File:

PDF, 12.15 MB

english, 2017

2

A Nanoscale Ion Pump Derived From a Biological Water Channel

Decker, Karl, Page, Martin Anthony, Aksimentiev, Aleksei

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 8.46 MB

english, 2017

3

How Pegylation Stabilizes a Protein

Chao, Shu-Han, Price, Joshua, Aksimentiev, Aleksei, Gruebele, Martin

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

4

Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

Yoo, Jejoong, Aksimentiev, Aleksei

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 4.95 MB

english, 2015

5

Sequence-dependent DNA condensation as a driving force of DNA phase separation

Kang, Hyunju, Yoo, Jejoong, Sohn, Byeong-Kwon, Lee, Seung-Won, Lee, Hong Soo, Ma, Wenjie, Kee, Jung-Min, Aksimentiev, Aleksei, Kim, Hajin

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 6.20 MB

english, 2018

6

Molecular Transport across the Ionic LiquidâAqueous Electrolyte Interface in a MoS 2 Nanopore

Shankla, Manish, Aksimentiev, Aleksei

Journal:

ACS Applied Materials & Interfaces

Year:

2020

File:

PDF, 18.29 MB

2020

7

Lipid bilayer coated Al2O3nanopore sensors: towards a hybrid biological solid-state nanopore

Bala Murali Venkatesan, James Polans, Jeffrey Comer, Supriya Sridhar, David Wendell, Aleksei Aksimentiev, Rashid Bashir

Journal:

Biomedical Microdevices

Year:

2011

Language:

english

File:

PDF, 825 KB

english, 2011

8

DNA Sequence-Dependent Ionic Currents in Ultra-Small Solid-State Nanopores

Comer, Jeffrey R, Aksimentiev, Aleksei

Journal:

Year:

2016

Language:

english

File:

PDF, 7.00 MB

english, 2016

9

The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

Shi, Xin, Li, Qiao, Gao, Rui, Si, Wei, Liu, Shao-Chuang, Aksimentiev, Aleksei, Long, Yi-Tao

Journal:

The Journal of Physical Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 1.15 MB

english, 2018

10

Step-defect guided delivery of DNA to a graphene nanopore

Shankla, Manish, Aksimentiev, Aleksei

Journal:

Nature Nanotechnology

Year:

2019

Language:

english

File:

PDF, 2.08 MB

english, 2019

11

Assessing Graphene Nanopores for Sequencing DNA

Wells, David B., Belkin, Maxim, Comer, Jeffrey, Aksimentiev, Aleksei

Journal:

Year:

2012

Language:

english

File:

PDF, 3.52 MB

english, 2012

12

DNA Base-Calling from a Nanopore Using a Viterbi Algorithm

Timp, Winston, Comer, Jeffrey, Aksimentiev, Aleksei

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 396 KB

english, 2012

13

Sizing DNA Using a Nanometer-Diameter Pore

Heng, Jiunn B., Ho, Chuen, Kim, Taekyung, Timp, Rolf, Aksimentiev, Aleksij, Grinkova, Yelena V., Sligar, Stephen, Schulten, Klaus, Timp, Gregory

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 325 KB

english, 2004

14

Modeling transport through synthetic nanopores

Aksimentiev, A., Brunner, R., Cruz-Chu, E., Comer, J., Schulten, K.

Journal:

IEEE Nanotechnology Magazine

Year:

2009

Language:

english

File:

PDF, 2.34 MB

english, 2009

15

Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer

Maffeo, Christopher, Aksimentiev, Aleksei

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 2.99 MB

english, 2009

16

Nanopore Sequencing: Electrical Measurements of the Code of Life

Timp, Winston, Mirsaidov, Utkur M, Deqiang Wang,, Comer, Jeff, Aksimentiev, Aleksei, Timp, Gregory

Journal:

IEEE Transactions on Nanotechnology

Year:

2010

Language:

english

File:

PDF, 937 KB

english, 2010

17

‘At’ Content as a Determinant of the Chromosome Structure

Kim, Hajin, Yoo, Jejoong, Aksimentiev, Aleksei, Ha, Taekjip

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

18

Detecting SNPs Using a Synthetic Nanopore

Zhao, Q., Sigalov, G., Dimitrov, V., Dorvel, B., Mirsaidov, U., Sligar, S., Aksimentiev, A., Timp, G.

Journal:

Year:

2007

Language:

english

File:

PDF, 1.19 MB

english, 2007

19

Control and reversal of the electrophoretic force on DNA in a charged nanopore

Luan, Binquan, Aksimentiev, Aleksei

Journal:

Journal of Physics Condensed Matter

Year:

2010

Language:

english

File:

PDF, 931 KB

english, 2010

20

Quantification of Membrane Protein-Detergent Complex Interactions

Wolfe, Aaron John, Si, Wei, Zhang, Zhengqi, Blanden, Adam R, Hsueh, Yi-Ching, Gugel, Jack Fredrick, Pham, Bach, Chen, Min, Loh, Stewart N, Rozovsky, Sharon, Aksimentiev, Aleksei, Movileanu, Liviu

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 7.17 MB

english, 2017

21

Single molecule force measurements: Insights from molecular simulations: Comment on “Biophysical characterization of DNA binding from single molecule force measurements” by Kathy R. Chaurasiya et al.

Christopher Maffeo, Aleksei Aksimentiev

Journal:

Physics of Life Reviews

Year:

2010

Language:

english

File:

PDF, 68 KB

english, 2010

22

Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor

Sigalov, Grigori, Comer, Jeffrey, Timp, Gregory, Aksimentiev, Aleksei

Journal:

Year:

2008

Language:

english

File:

PDF, 494 KB

english, 2008

23

Modeling Pressure-Driven Transport of Proteins Through a Nanochannel

Carr, Rogan, Comer, Jeffrey, Ginsberg, Mark D., Aksimentiev, Aleksei

Journal:

IEEE Transactions on Nanotechnology

Year:

2011

Language:

english

File:

PDF, 501 KB

english, 2011

24

Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends

Aksimentiev, Aleksij, Hołyst, Robert

Journal:

Physical Review E

Year:

2000

Language:

english

File:

PDF, 154 KB

english, 2000

25

Strain Softening in Stretched DNA

Luan, Binquan, Aksimentiev, Aleksei

Journal:

Physical Review Letters

Year:

2008

Language:

english

File:

PDF, 988 KB

english, 2008

26

Highly permeable artificial water channels that can self-assemble into two-dimensional arrays

Shen, Yue-xiao, Si, Wen, Erbakan, Mustafa, Decker, Karl, De Zorzi, Rita, Saboe, Patrick O., Kang, You Jung, Majd, Sheereen, Butler, Peter J., Walz, Thomas, Aksimentiev, Aleksei, Hou, Jun-li, Kumar, Ma

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

27

The structure and intermolecular forces of DNA condensates

Yoo, Jejoong, Aksimentiev, Aleksei

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 8.40 MB

english, 2016

28

The Electromechanics of DNA in a Synthetic Nanopore

Heng, J.B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y.V., Sligar, S., Schulten, K., Timp, G.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 623 KB

english, 2006

29

Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface

Carr, Rogan, Comer, Jeffrey, Ginsberg, Mark D., Aksimentiev, Aleksei

Journal:

The Journal of Physical Chemistry Letters

Year:

2011

Language:

english

File:

PDF, 3.58 MB

english, 2011

30

Membrane-Spanning DNA Ion Channels: Conductance Mechanism, Electro-Osmotic Transport and Mechanical Gating

Yoo, Jejoong, Li, Chen-Yu, Aksimentiev, Aleksei

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 45 KB

english, 2016

31

Microcarrier-Guided Nanopore Dielectrophoresis for Selective Nucleic Acid Detection

Tian, Kai, Decker, Karl, Aksimentiev, Aleksei, Gu, Liqun

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 42 KB

english, 2016

32

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Yoo, Jejoong, Kim, Hajin, Aksimentiev, Aleksei, Ha, Taekjip

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

33

Unraveling the Nucleosome through Microscopic Simulations

Winogradoff, David N., Aksimentiev, Aleksei

Journal:

Biophysical Journal

Year:

2020

Language:

english

File:

PDF, 41 KB

english, 2020

34

Multi-Resolution Model of the Eukaryotic Cytoplasm

Chou, Han-Yi, Winogradoff, David N., Maffeo, Christopher M., Aksimentiev, Aleksei

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

35

Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends

Aksimentiev, Aleksij, Moorthi, Krzysztof, Holyst, Robert

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 645 KB

english, 2000

36

Slowing DNA Transport Using Graphene-DNA Interactions

Banerjee, Shouvik, Wilson, James, Shim, Jiwook, Shankla, Manish, Corbin, Elise A., Aksimentiev, Aleksei, Bashir, Rashid

Journal:

Advanced Functional Materials

Year:

2015

Language:

english

File:

PDF, 2.48 MB

english, 2015

37

PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore

Chowdhury, Ratul, Ren, Tingwei, Shankla, Manish, Decker, Karl, Grisewood, Matthew, Prabhakar, Jeevan, Baker, Carol, Golbeck, John H., Aksimentiev, Aleksei, Kumar, Manish, Maranas, Costas D.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.63 MB

english, 2018

38

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

Ohayon, Shilo, Girsault, Arik, Nasser, Maisa, Shen-Orr, Shai, Meller, Amit, Aksimentiev, Aleksei

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 8.43 MB

english, 2019

39

Stretching DNA Using the Electric Field in a Synthetic Nanopore

Heng, Jiunn B., Aksimentiev, Aleksei, Ho, Chuen, Marks, Patrick, Grinkova, Yelena V., Sligar, Steve, Schulten, Klaus, Timp, Gregory

Journal:

Year:

2005

Language:

english

File:

PDF, 487 KB

english, 2005

40

A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment

Maffeo, Christopher, Ngo, Thuy T. M., Ha, Taekjip, Aksimentiev, Aleksei

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.08 MB

english, 2014

41

Electro-osmotic screening of the DNA charge in a nanopore

Luan, Binquan, Aksimentiev, Aleksei

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

42

Smooth DNA Transport through a Narrowed Pore Geometry

Carson, Spencer, Wilson, James, Aksimentiev, Aleksei, Wanunu, Meni

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 2.18 MB

english, 2014

43

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores

Belkin, Maxim, Aksimentiev, Aleksei

Journal:

ACS Applied Materials & Interfaces

Year:

2016

Language:

english

File:

PDF, 3.97 MB

english, 2016

44

Large-Conductance Transmembrane Porin Made from DNA Origami

Göpfrich, Kerstin, Li, Chen-Yu, Ricci, Maria, Bhamidimarri, Satya Prathyusha, Yoo, Jejoong, Gyenes, Bertalan, Ohmann, Alexander, Winterhalter, Mathias, Aksimentiev, Aleksei, Keyser, Ulrich F.

Journal:

Year:

2016

Language:

english

File:

PDF, 5.32 MB

english, 2016

45

In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin

Vadim Cherezov, Wei Liu, Jeremy P. Derrick, Binquan Luan, Aleksei Aksimentiev, Vsevolod Katritch, Martin Caffrey

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 288 KB

english, 2008

46

Modeling and Simulation of Ion Channels

Maffeo, Christopher, Bhattacharya, Swati, Yoo, Jejoong, Wells, David, Aksimentiev, Aleksei

Journal:

Chemical Reviews

Year:

2012

Language:

english

File:

PDF, 16.97 MB

english, 2012

47

Rectification of the Current in α-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments

Bhattacharya, Swati, Muzard, Julien, Payet, Linda, Mathé, Jerome, Bockelmann, Ulrich, Aksimentiev, Aleksei, Viasnoff, Virgile

Journal:

The Journal of Physical Chemistry C

Year:

2011

Language:

english

File:

PDF, 2.86 MB

english, 2011

48

MORPHOLOGICAL TRANSFORMATIONS DURING PHASE-SEPARATION/ORDERING PHENOMENA

Aksimentiev, Aleksij

Journal:

Molecular Crystals and Liquid Crystals Science and Technology Section A Molecular Crystals and Liquid Crystals

Year:

2001

Language:

english

File:

PDF, 410 KB

english, 2001

49

Plasmonic Nanopores for Trapping, Controlling Displacement and Sequencing of DNA Molecules

Belkin, Maxim, Chao, Shu Han, Jonsson, Magnus P., Dekker, Cees, Aksimentiev, Aleksei

Journal:

Year:

2015

Language:

english

File:

PDF, 2.65 MB

english, 2015

50

Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

Slone, Scott Michael, Li, Chen-Yu, Yoo, Jejoong, Aksimentiev, Aleksei

Journal:

New Journal of Physics

Year:

2016

Language:

english

File:

PDF, 2.16 MB

english, 2016

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