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The Aksimentiev Group
Theoretical and Computational Research at the Interface of Physics, Biology, and Nanotechnology
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Aleksei Aksimentiev
Behzad Mehrafrooz
Christopher Maffeo
Hemani Chhabra
Jingqian Liu
Kumar Sarthak
Kush Coshic
Parth Chaturvedi
Pin-Yi Li
Siddharth Krishnan
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DNA–DNA interactions
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CUFIX: Champaign-Urbana Non-bonded Fix (NBFIX)
Atomic Resolution Brownian Dynamics
Grid-steered molecular dynamics
Tutorials
Bionanotechnology Tutorial
Electrostatic Maps and Ion Conduction
Introduction to MD simulation of DNA-protein systems
Membrane Proteins Tutorial
Modeling Nanopores for Sequencing DNA
Modeling Synthetic Ion Channels with Coarse-Grained Molecular Dynamics
Rendering with Tachyon
User-Defined Forces in NAMD
VMD Images and Movies Tutorial
Visualizing MD Results: Stretching dsDNA Mini Tutorial
A Practical Guide to DNA Origami Simulations Using NAMD
Analyzing DNA Flexibility
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Author
any
Abramkina, Volha
Acuna, Guillermo P
Afonin, Kirill A.
Aksimentiev, Aleksei
Aksimentiev, Aleksei
Alfaro, Javier Antonio
Alford, Aaron
Ali, Noor
Alibakhshi, Mohammad Amin
Anslyn, Eric V.
Antson, Alfred A.
Arai, Tatsuo
Arkhipov, Anton
Arnott, Patrick M.
Baker, Carol
Balabin, Ilya A
Banerjee, Shouvik
Bashir, Rashid
Baumann, Kevin N.
Bedran, Georges
Behera, Harekrushna
Behrends, Jan C.
Behrends, Jan C.
Belkin, Maxim
Benabbas, Abdelkrim
Benson, Christopher R.
Bernardi, Rafael C.
Bertosin, Eva
Bhamidimarri, Satya Prathyusha
Bhattacharya, Swati
Bhattacharya, Swati
Birkedal, Victoria
Blanden, Adam R
Bockelmann, Ulrich
Boggs, David G.
Bohländer, Peggy
Boorla, Veda Sheersh
Boyd, Ashley
Bridwell-Rabb, Jennifer
Brinkerhoff, Henry
Brunner, Robert
Brutzer, Hergen
Buch, Ronak
Bui, Minh
Bui, Minh
Burdzy, Krzysztof
Burdzy, K
Burns, Jonathan R
Butler, James E
Butler, Peter J.
Büber, Ece
Caffrey, Martin
Cao, Chan
Carlisle, John A
Carr, Rogan
Carson, Spencer
Carson, Spencer
Chae, Inseok
Champion, Paul M
Chandak, Shubham
Chandler, Morgan
Chandler, Danielle E.
Chao, Shu-Han
Chao*, Shu-Han
Chaudhry, Jehanzeb Hameed
Chechik, Maria
Chen, Feng
Chen, Kaikai
Chen, Min
Cherezov, Vadim
Chinappi, Mauro
Chipot, Christophe
Chou, Han-Yi
Chou, Han-Yi
Choudhary, Adnan
Chowdhury, Ratul
Chowdhury, Ratul
Clare, Tami Lasseter
Cohen, Jordi
Coltan, David
Comer, Jeffrey
Corbin, Elise A.
Coshic, Kush
Coyaud, Etienne
Cremer, Paul S.
Cressiot*, Benjamin
Cropek, Donald
Cruz-Chú, Eduardo
Dai, Mingjie
Dai, Q
Dalal, Yamini
Dalal, Yamini
De Respino, Sophie
De Zorzi, Rita
Decker, Karl
Decker, Karl
Dekker, Cees
Dekker, Cees
Delgado-Magnero, Karelia H.
Derrick, Jeremy P
Derrington, Ian M
Dhiman, Raman
Di Michele, Lorenzo
Di Ventra, Massimiliano
Dietz, Hendrik
Dimitrov, Valentin
Dittmar, Gunnar
Dong, Lixin
Dorvel, B
Drachman, Nicholas
Drexler, Thomas
Drndic, Marija
Ducati, Caterina
Echeverria, Ignacia
Eelkema, Rienk
Eggert, Ulrike S
Elessawy, Nada
Ennslen, Tobias
Ensslen, Tobias
Eom, Kilho
Erbakan, Mustafa
Fallahi, Ali
Farell, Megan
Farell, Megan
Fatila, Elisabeth M.
Fatima, Saman
Feigl, Elija
Feng, Jiandong
Fenniri, Hicham
Fialkowski, Marcin
Filius, Mike
Fillingame, Robert H
Fiorin, Giacomo
Fitzgerald, Clare
Flood, Amar H.
Foster, Joshua C.
Fowle, William H
Franquelim, Henri G
Freddolino, Peter L
Freeman, Benny D.
Fukuda, Toshio
Gamble, Trevor
Gao, Jia
Gao, Rui
Gao, Luyu
Gao, Mu
Ge, Yingda
Geim, Andre K.
Giannetti, Gino
Ginsberg, Mark D
Ginsberg, Mark
Golbeck, John H
Golestanian, Ramin
Goodlett, David
Goodman, J S
Göpfrich, Kerstin
Göpfrich, Kerstin
Göpfrich*, Kerstin
Gracheva, Maria E.
Greive*, Sandra J.
Grinkova, Yelena V
Grisewood, Matthew
Gruebele, Martin
Gruebele, Martin
Gu, Li-Qun
Gugel, Jack Fredrick
Gumbart, James
Gundlach, Jens H
Gyenes, Bertalan
Ha, Taekjip
Ha, Taekjip
Halman, Justin R.
Halman, Justin
Hamers, Robert J
Hardy, David
Hardy, David J.
He, Zhiren
He, C
Hecker, Lisa
Hemmig, Elisa A.
Hemmig, Elisa Alina
Henderson, Codey B.
Heng, Jiunn B
Hénin, Jérôme
Hentz, Sébastien
Hernandez, Alvaro G
Hernández-Ainsa, Silvia
Hickey, Robert J.
Hitchcock, Andrew
Ho, C
Ho, Chuen
Ho, Anthony H.
Holyst, Robert
Honemann, Maximilian N
Hou, Jun-li
Hou, Sen
Howard, Cecil J.
Howorka, Stefan
Hołyst, Robert
Hsueh, Yi-Ching
Huang, Qiang
Huang, Feihe
Huijben, Teun
Hunter, Neil
Hübner, Kristina
Iqbal, Samir
Iqbal, Samir M.
Isralewitz, Barry
Isralewitz, Barry
Jackson, Sophie E.
Jenkins, Huw Thomas
Jepsen, Mette D. E.
Jiang, Wei
John, Shalini
John*, Shalini
Jones, Sioned F
Jonsson, Magnus P.
Joo, Chirlmin
Joo, Chirlmin
Joshi, H
Joshi, Himanshu
Joshi, Himanshu
Kalathiya, Umesh
Kalé, Laxmikant V.
Kang, You Jung
Kang, Hyunju
Kang, Albert SW
Kang, Xinqi
Katritch, Vsevolod
Kee, Jung-Min
Keerthi, Ashok
Kelleher, Neil L.
Kelly, Ryan T.
Kelman, Zvi
Kemper, Ulrich
Kennard, Celeste
Keyser, Ulrich F
Keyser, Ulrich F.
Keyser, Ulrich F
Kharlampieva, Eugenia
Kher, Kartik
Kim, Hajin
Kim, Eunjung
Kim, Seong H.
Kim, Sung Hyun
Kim, Taekyung
King, William P
Kjems, Jørgen
Kleinekathöfer, Ulrich
Kohler, Fabian
Kojima, Masaru
Kong, Jinglin
Kowalczyk, Stefan W
Kozlovskaya, Veronika
Krishnan, Siddharth
Kubalski, Andrzej
Kumar, Manish
Kumar, Manish
Kuster, Bernhard
Lang, Chao
Leburton, Jean-Pierre
Lee, Seung-Won
Lee, Hong Soo
Lenting, Erica Mariska
Li, Zhongyan
Li, Chen-Yu
Li, Ning
Li, Yi
Li, Sheng
Li, Lin
Li, Qiao
Li, Fanjun
Li, Chen-Yu
Li, Pin‐Yi
Li*, Chen-Yu
Lin, Yi-Chih
Lin, Chunchen
Lindsay, Stuart
Lindsay, Stuart
Liu, Yun
Liu, Fengyu
Liu, Jingqian
Liu, Chang
Liu, Xiaoming
Liu, Wei
Liu, Shao-Chuang
Liu, Jingqian
Loh, Stewart N
Long, Yi-Tao
Lopez-Marques, Horacio
Lu, Deyu
Lu, Xueguang
Luan, B
Luan, Binquan
Lucas, Florian Leonardus
Luthey-Schulten, Zaida
Ma, Wenjie
MacAllister, Irene
Maffeo, Christopher
Maffeo, C
Maffeo, Christopher M
Maffeo, Christopher Michael
Maffeo, Christopher
Maglia, Giovanni
Maglia, Giovanni
Maia, Julio D. C.
Majd, Sheereen
Makhamreh, Amr
Mallus, Ilaria
Mames, Adam
Mames, Iwona
Manivet, Philippe
Mansfield, W
Maranas, Costas D.
Maranas, Costas D
Maranas, Costas
Marcotte, Edward M.
Marino, John P.
Marks, Patrick
Martinac, Boris
Masselon, Christophe
Massenburg, Lynnicia
Mathé, Jérôme
Matthews, Sam S
Matyushov, Dmitry
Mayer, Michael
McGreevy, Ryan
Mehrafrooz, Behzad
Meller, Amit
Meller, Amit
Melo, Marcelo C. R.
Ménard, Brice
Mettela, Gangaiah
Milenkovic, Olgica
Miner, J
Mirsaidov, U
Mirsaidov, Utkur
Mirsaidov, Utkur M
Mojtabavi, Mehrnaz
Moorthi, Krzysztof
Morzy, Diana
Movileanu, Liviu
Müller, Achim
Muzard, L
Myong, Sua
Nahas, Kareem Al
Najem, Joseph S.
Nelson, David R
Ngo, Thuy T. M.
Ngo, Thuy
Nguyen, Jonathan
Niederweis, Michael
Ochmann, Sarah Elisabeth
Ochmann, Sarah E
Oh, Hyeonji
Ohayon, Shilo
Ohmann, Alexander
Ohmann, Alexander
Olshansky, Lisa
Olson, Luke N
Oukhaled, Abdelghani
Ouldali, Hadjer
Page, Martin
Pan, Chao
Pandey, Laxmi
Papoian, Garegin A
Papoian, Garegin
Park, Sangwoo
Pascoa, Tomas
Pavlenok, Mikhail
Paxman, Ryan
Payet, Linda
Pelta, Juan
Penkauskas, Tadas
Pevarnik, Matthew
Pham, Bach
Phillips, James C.
Phillips, James C
Pietschmann, Jan-Frederik
Piguet, Fabien
Pitz, Megan E.
Plett, Timothy S.
Plewczyński, D
Pogorelov, Taras V.
Pogorelov, Taras V
Pogorelov, T V
Polans, James
Pomorski, Adam
Potoyan, Davit A
Prabhakar, Jeevan
Price, Joshua L
Prigozhin*, Maxim B
Pud, Sergii
Pumm, Anna-Katharina
Qian, Shuo
Qiao, Dan
Quednau, L
Quednau, Lauren
R, Deepa
Radadia, Adarsh D
Radak, Brian K.
Radha, Boya
Rajan, Aruna
Ranson, Neil A
Reibetanz, Uta
Reiner, Joseph E.
Ren, Tingwei
Ren, Changliang
Restrepo-Perez, Laura
Restrepo-Perez*, Laura
Ribeiro, João V.
Ricci, Maria
Robertson, Joseph W. F.
Robinson, Joshua
Rodriguez-Larrea, David
Roux, Benoît
Roy, Arundhati
Rozovsky, Sharon
Rubio-Sánchez, Roger
Ruijuan, Ye
Saboe, Patrick O.
Saccà, Barbara
Samaras, Patroklos
Samineni, Laxmicharan
Samineni, Laximicharan
Samori, Bruno
Sandler, Sarah E.
Sarles, Stephen A.
Sarthak, Kumar
Sarthak, Kumar
Scheffler, Florian
Scherf, Merle
Schmid, Sonja
Schöpflin, Robert
Schroeder, Charles M
Schulman, Rebecca
Schulten, Klaus
Scrimgeour, Jan
Seidel, Ralf
Seidel, Ralf
Sener, Melih
Sepiashvili, Lusia
Shankla, Manish
Shankla, Manish
Sheetz, Edward G.
Shen, Jie
Shen, Yue-xiao
Shi, Qing
Shi, Xin
Shi, Xin
Shih, Amy Y
Shim, Jiwook
Shorkey, Spencer A
Shuai, Liang
Si, Wei
Si, Wei
Si, Wen
Si*, Wei
Sigalov, G
Singh, Swapnil
Singharoy, Abhishek
Singharoy, Abhishek
Sivaprasadarao, Asipu
Siwy, Zuzanna S.
Siwy, Zuzanna S
Skeel, Robert D.
Skiles, Matthew
Sligar, S
Sloman, Leila
Slone, Scott Michael
Sobota, Diana
Sohn, Byeong-Kwon
Song, Woochul
Song, Woochul
Sorsch, T
Soskine, Misha
Sotomayor, Marcos
Sridhar, Supriya
Stavis, Courtney J
Stefani, Fernando D
Stegemann, Pierre
Stehr, René
Stein, Derek
Stone, John E.
Stulz, Eugen
Subramanian, Shruti
Sukenik, Shahar
Sun, Lili
Swainsbury, David J.K.
Sørensen, Rasmus Schøler
Tabaka, Marcin
Tabatabaei, Kasra
Tajkhorshid, Emad
Tajkhorshid, Emad
Teo, Ivan
Terry, Stephen J
Thielges, Megan C.
Thompson, Rebecca F
Tian, Kai
Tieleman, Peter
Timp, Winston
Timp, Gregory
Timp, Rolf
Tinnefeld, Philip
Tor, Yitzhak
Tripathi, Prabhat
Tu, Yu-Ming
Tu, Yu-Ming
Uline, Mark J.
Urban, Volker
van der Heide, Nieck Jordy
van Engelenburg, Casper
van Kooten, Xander F.
Vant, John W.
Venkatesan, Bala Murali
Verschueren, Daniel
Verschueren, Daniel
Versloot, Roderick Corstiaan
Viasnoff, Virgile
Vlassiouk, Ivan
Walz, Thomas
Wang, Deqiang
Wang, Yi
Wang, Fushi
Wang, Qian
Wang, Yi
Wanunu, Meni
Wanunu, Meni
Wedemann, Gero
Wei, Xiaojun
Weigele, Peter R.
Weinstock, Ira A
Wells, D B
Wells, David B
Wendell, David
Wetherington, Maxwell
Wilhelm, Mathias
Wilson, James
Wilson, James
Wilson, James
Winogradoff, David
Winogradoff, David
Winogradoff, D
Winogradoff*, David
Winterhalter, Mathias
Wolfe, Aaron John
Xie, Yun
Xiong, A.
Xu, Yang
Yamazaki, Hirohito
Yang, Wayne
Yang, Yiming
Ye, Jingjing
Ye, Ruijuan
Yemenicioglu, S
Yin, Peng
Yin, Ying
Yoo, Jejoong
Yoo, J
Yoo, Jejoong
You, Yi
Yu, Luning
Zeng, Hongjun
Zeng, Huaqiang
Zhang, Q
Zhang, Zhengqi
Zhang, Ke
Zhang, Xuzhu
Zhao, Q
Zhao, Qian
Zhao, Shidi
Zhao, Wenxuan
Zhao, Shidi
Zhao, Haiqing
Zhao*, Haiqing
Zhu, Huangtianzhi
Zhu, Fangqiang
Zou, Xueqing
Zuccheri, Giampaolo
Zwolak, Michael
Type
any
Journal Article
Book Chapter
Term
any
Year
any
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
2000
1999
1998
Keyword
any
2D nanoslits
Adhesins, Bacterial
Algorithms
Aluminum Oxide
Amino Acid Motifs
Amino Acid Sequence
Anti-Bacterial Agents
Antibodies, Bacterial
Aquaporins
Arginine
Avidin
Bacterial Outer Membrane Proteins
Bacterial Proteins
Bacterial Toxins
Bacteriophage lambda
Base Pairing
Base Sequence
Binding Sites
Binding, Competitive
bioenergetics
biological membranes
Biological Transport
Biomechanical Phenomena
Biophysical Phenomena
Biophysics
biopolymers
biosensing
Biosensing Techniques
Biotechnology
Boundary-driven MD
Calcium
Calcium-Binding Proteins
Catalysis
Cations
Cell Membrane
Cell Membrane Permeability
Centromere Protein A
charge transport
Chemical Engineering
Chemistry, Physical
cholesterol-modified DNA nanostructures,
chromatophore
coarse-grained simulation
Comparison between biological and synthetic nanopores
Computational Biology
Computational biophysics
Computer Simulation
Conductometry
Cryoelectron Microscopy
Crystallography, X-Ray
Cytoplasm
Deoxyribonuclease BamHI
Deoxyribonuclease EcoRI
Diamond
Diffusion
Dimerization
DNA
DNA damage
DNA Methylation
DNA Mutational Analysis
DNA nanostructures
DNA Nanotechnology
DNA packaging
DNA repair
DNA structures
DNA translocation
DNA, Circular
DNA, Single-Stranded
DNA, Superhelical
DNA, Viral
DNA-Binding Proteins
DNA-PAINT
dodecane
Elasticity
Electric Conductivity
Electrical conductivity
Electricity
Electrochemical Techniques
Electrochemistry
Electrolytes
Electromagnetic Fields
Electroosmosis
Electrophoresis
Electrophoresis, Agar Gel
Electrophysiology
Electroporation
Escherichia coli K12
Escherichia coli Proteins
Ethylene Glycol
Fibrinogen
Fibronectins
Fluorescence
Fluorescence Recovery After Photobleaching
Fluorescent Dyes
Foldamers
Gene delivery
Genetics
Genome, Human
graphene
graphene–DNA interactions
Graphite
H-Bonds
HeLa Cells
Hemolysin Proteins
Histones
homologous recombination
Humans
Hydrodynamic focusing
Hydrogen Bonding
Hydrogen-Ion Concentration
Hydrophobic and Hydrophilic Interactions
integrative model
Ion Channel Gating
Ion Channels
Ion Transport
ionic current
Ions
Kinetics
Lipid Bilayer anchored DNA
Lipid Bilayers
lipid flipping
lipid membranes
Lipid-DNA binding affinity
Liposomes
Lithium Channels
Lithium Chloride
Macromolecular Substances
Markov Chains
Materials Testing
MD
MD Simulations
membrane
Membrane biophysics
Membrane Potentials
Membrane Proteins
Membrane Transport Proteins
Membranes
Membranes, Artificial
Metals
Micelles
Microelectrodes
Microfluidic Analytical Techniques
Microscopy, Atomic Force
Microscopy, Electron, Transmission
Microtubules
mitochondria
Models, Biological
Models, Chemical
Models, Genetic
Models, Molecular
Models, Statistical
Models, Theoretical
Molecular Conformation
Molecular dynamics
Molecular Dynamics Simulation
Molecular dynamics simulations
Molecular Motor Proteins
Molecular Sequence Data
Molecules
Monomers
Monte Carlo Method
Motion
Multiresolution simulation
Mutation
Nanobiotechnology
Nanocapsules
nanochannel
Nanofluidics
nanopore sequencing
Nanopores
Nanostructures
Nanotechnology
Nanotubes
Nanotubes, Carbon
Neisseria meningitidis
nicks
Non-equilibrium MD
NPC
nuclear pore
Nucleic Acid Conformation
nucleic acids
optical spectroscopy
Organic Nanotubes
Osmosis
Oxides
Paromomycin
Particle Size
passive transport
Permeability
permeation
Phosphates
Phosphatidylcholines
Photoelectron Spectroscopy
photosynthesis
Plasmonic heating
Poly A
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Porins
Porosity
Potassium Ions Selectivity
Protein Binding
Protein Conformation
Protein Denaturation
Protein Folding
Protein Multimerization
Protein Structure, Quaternary
Protein Structure, Secondary
Protein Structure, Tertiary
Protein Subunits
protein-mimicking
Proteins
Proteoglycans
Proton-Translocating ATPases
Protons
QM/MM
replisome
Reproducibility of Results
Review
RNA
Rotation
Salts
Semiconductors
Sensitivity and Specificity
Sequence Analysis
Sequence Analysis, DNA
Sequencing DNA
Signal-To-Noise Ratio
Silicon
Silicon Compounds
Silicon Dioxide
single molecule
Single-molecule fluorescence polarization-resolved microscopy
Sodium Chloride
Solvents
Soret coefficient
Spectrum Analysis
stacked membranes
Staining and Labeling
Static Electricity
Stochastic Processes
Stress, Mechanical
Substrate Specificity
super resolution
Super-resolution microscopy
Supramolecular Chemistry
Surface Properties
synthetic ion channel
Thermodiffusion
Thermodynamics
Thermophoresis
tilt
Time Factors
Titanium
Translocation, Genetic
transmembrane transport
Trapping DNA
Tryptophan
Tubulin
Tungsten Compounds
Tyrosine
Ultrafiltration
virology
Vitamin B 12
Vitamin B Complex
Water
λ-DNA
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