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List of works by Aleksei Aksimentiev

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

scientific article

A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore

scientific article published on January 2014

A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes.

scientific article

Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore

scientific article published on 11 May 2009

Artificial water channels enable fast and selective water permeation through water-wire networks

scientific article published on 16 December 2019

Assessing graphene nanopores for sequencing DNA.

scientific article

Atoms-to-microns model for small solute transport through sticky nanochannels

scientific article

Author Correction: Artificial water channels enable fast and selective water permeation through water-wire networks

scientific article published on 01 February 2020

Beyond the Gene Chip

article

Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures

scientific article published in 2021

Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features

scientific article published on 18 March 2019

Close encounters with DNA

scientific article

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations ⬇️

scientific article published on October 19, 2012

Computer modeling in biotechnology: a partner in development

scientific article

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

scientific article

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

scientific article

Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces

scientific article

Controlling aggregation of cholesterol-modified DNA nanostructures

scientific article published on 01 December 2019

Correction to Ion Channels Made from a Single Membrane-Spanning DNA Duplex

scientific article published on 13 June 2017

DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity

DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity

DNA attraction in monovalent and divalent electrolytes

scientific article published on November 2008

DNA base-calling from a nanopore using a Viterbi algorithm

scientific article published on 15 May 2012

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

scientific article published on 01 November 2021

DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

scientific article published on 22 April 2016

DNA-DNA interactions in tight supercoils are described by a small effective charge density

scientific article published on 4 October 2010

De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

scientific article published on 14 March 2016

Deciphering ionic current signatures of DNA transport through a nanopore

scientific article

Detecting SNPs using a synthetic nanopore

scientific article

Detection of DNA sequences using an alternating electric field in a nanopore capacitor

scientific article

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

scientific article published on 22 March 2016

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes

article

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

scientific article published on 03 August 2018

Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes

scientific article published on 21 February 2019

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

scientific article published on 24 February 2016

Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes

scientific article

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

scientific article published on 16 December 2019

Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor

article by Maria E Gracheva et al published 5 June 2006 in Nanotechnology

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

scientific article published on 8 February 2019

Electro-osmotic screening of the DNA charge in a nanopore

scientific article

End-to-end attraction of duplex DNA.

scientific article

Exploring the Prospects for a Nanometer-scale Gene Chip

article

Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics

scientific article

Graphene Nanopores for Protein Sequencing

scientific article published on 09 June 2016

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System

scientific article published on 11 November 2020

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

scientific article

Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.

scientific article published on 17 November 2015

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

scientific article published on 2 December 2015

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

article

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

scientific article published on 4 May 2016

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

scientific article

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

scientific article

Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem

article published in the Proceedings of the National Academy of Sciences of the United States of America

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

scientific article

Ion Channels Made from a Single Membrane-Spanning DNA Duplex

scientific article

Ionic Current Rectification Through Silica Nanopores

scientific article

Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field ⬇️

scientific article

Large-Conductance Transmembrane Porin Made from DNA Origami

scientific article (publication date: 27 September 2016)

Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore

scientific article

Mechanical properties of a complete microtubule revealed through molecular dynamics simulation

scientific article

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure

Membrane activity of a DNA-based ion channel depends on the stability of its double-stranded structure

Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface

scientific article

Microscopic mechanics of hairpin DNA translocation through synthetic nanopores

scientific article published on January 2009

Modeling Pressure-Driven Transport of Proteins through a Nanochannel

scientific article

Modeling Transport Through Synthetic Nanopores

scientific article

Modeling and simulation of ion channels

scientific article

Modeling thermophoretic effects in solid-state nanopores

scientific article

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor

scientific article published on 23 December 2016

Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores

scientific article published on 10 March 2016

Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

scientific article published on 9 November 2015

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

scientific article published on 12 February 2019

Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence

scientific article

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

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

scientific article published on 31 March 2020

Multiple rereads of single proteins at single-amino acid resolution using nanopores

Nanopore Sensing of Protein Folding

scientific article published on 10 July 2017

Nanopore Sequencing: Electrical Measurements of the Code of Life

scientific article

Nanopore Sequencing: Graphene Nanopores for Protein Sequencing (Adv. Funct. Mater. 27/2016)

Nanopore analysis of individual RNA/antibiotic complexes

scientific article published on 16 November 2011

Nanoscale Ion Pump Derived from a Biological Water Channel

scientific article published on 26 July 2017

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

scientific article published on 16 March 2018

Optical Voltage Sensing Using DNA Origami.

scientific article published on 12 February 2018

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores

scientific article published in January 2012

Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel

scientific article

Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates

Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores.

scientific article

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

scientific article

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

scientific article published in Nature Communications

Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization.

scientific article published on 9 November 2017

Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics

scientific article

Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

scientific article published on 21 February 2020

Quantification of Membrane Protein-Detergent Complex Interactions

scientific article published on 16 October 2017

Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model

scientific article published on 13 March 2019

Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling

scientific article

Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments

scientific article

Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

scientific article published on 12 September 2016

Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors

scientific article published on 16 January 2020

SDS-assisted protein transport through solid-state nanopores

scientific article

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

scientific article published on 01 July 2020

Scaling of the Euler Characteristic, Surface Area, and Curvatures in the Phase Separating or Ordering Systems

scientific article published in Physical Review Letters

Selective Permeability of Truncated Aquaporin 1 in Silico

article published in 2017

Simulation of the electric response of DNA translocation through a semiconductor nanopore–capacitor

article

Single molecule analysis of structural fluctuations in DNA nanostructures

scientific article published on 01 October 2019

Single molecule force measurements: Insights from molecular simulations

Single-chain statistics in polymer systems

Slowing DNA Transport Using Graphene-DNA Interactions.

scientific article

Slowing down DNA translocation through a nanopore in lithium chloride

scientific article

Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

scientific article

Smooth DNA transport through a narrowed pore geometry

scientific article

Step-defect guided delivery of DNA to a graphene nanopore

scientific article published on 05 August 2019

Strain softening in stretched DNA.

scientific article published on 10 September 2008

Stretching DNA using the electric field in a synthetic nanopore

scientific article published on October 2005

Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores

scientific article published on 26 July 2013

Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

scientific article published on 21 January 2008

Structure refinement of the OpcA adhesin using molecular dynamics

scientific article

Structure, dynamics, and ion conductance of the phospholamban pentamer

scientific article published on June 2009

Super‐Resolution Detection of DNA Nanostructures Using a Nanopore

Surface functionalization of thin-film diamond for highly stable and selective biological interfaces

scientific article

Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes

scientific article

Tailoring Interleaflet Lipid Transfer with a DNA-based Synthetic Enzyme

scientific article published on 06 May 2020

The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study

scientific article

The effect of calcium on the conformation of cobalamin transporter BtuB.

scientific article

The electromechanics of DNA in a synthetic nanopore

scientific article

The role of molecular modeling in bionanotechnology

scientific article

The structure and intermolecular forces of DNA condensates

scientific article published on 15 February 2016

Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations

scientific article

Two structural scenarios for protein stabilization by PEG.

scientific article published on 2 June 2014

Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore

scientific article published on 7 April 2016

Water-silica force field for simulating nanodevices

scientific article

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