Makarov, Dmitrii E
Publication with MATCHING institution:
- Makarov DE (2009) Computer simulations and theory of protein translocation. Accounts of Chemical Research. [IF=3.533,
Cited=27, 19072704].
- Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, ..., Movileanu L (2007) Single-molecule electrophoresis of beta-
hairpin peptides by electrical recordings and Langevin dynamics simulations. Journal of Physical Chemistry B. [IF=0.893,
Cited=50, 17388500].
- Renn JP, Bhattacharyya S, Bai H, ..., Matouschek A (2019) Mechanical unfolding of spectrin reveals a super-exponential
dependence of unfolding rate on force. Scientific Reports. [IF=1.312, Cited=4, 31366931].
- Kirmizialtin S, Ganesan V, Makarov DE (2004) Translocation of a beta-hairpin-forming peptide through a cylindrical
tunnel. Journal of Chemical Physics. [IF=1.184, Cited=32, 15549903].
- Huang L, Makarov DE (2008) The rate constant of polymer reversal inside a pore. Journal of Chemical Physics. [IF=1.184,
Cited=20, 18361614].
- Lu CY, Makarov DE, Henkelman G (2010) Communication: κ-dynamics--an exact method for accelerating rare event classical
molecular dynamics. Journal of Chemical Physics. [IF=1.184, Cited=5, 21133434].
- Makarov DE, Rodin GJ (2002) Configurational entropy and mechanical properties of cross-linked polymer chains:
implications for protein and RNA folding. None. [IF=None, Cited=7, 12241385].
- Makarov DE (2014) Computational and theoretical insights into protein and peptide translocation. Protein and Peptide
Letters. [IF=0.422, Cited=4, 24370258].
Publication with MISMATCHING institution:
- Levy RM, Dai W, Deng NJ, Makarov DE (2013) How long does it take to equilibrate the unfolded state of a protein? Protein
Science. [IF=1.97, Cited=12, 23963761].
- Nam GM, Makarov DE (2015) Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force
spectroscopy experiments. Protein Science. [IF=1.97, Cited=22, 26088347].
- Makarov DE (2009) A theoretical model for the mechanical unfolding of repeat proteins. Biophysical Journal. [IF=0.842,
Cited=11, 19289042].
- Berezhkovskii AM, Makarov DE (2021) On distributions of barrier crossing times as observed in single-molecule studies of
biomolecules. Biophysical Reports. [IF=0.74, Cited=2, 36425456].
- Terterov I, Nettels D, Makarov DE, Hofmann H (2023) Time-resolved burst variance analysis. Biophysical Reports.
[IF=0.74, Cited=1, 37559939].
- Ma P, Elber R, Makarov DE (2020) Value of Temporal Information When Analyzing Reaction Coordinates. Journal of Chemical
Theory and Computation. [IF=1.512, Cited=5, 32841001].
- Satija R, Das A, Mühle S, ..., Makarov DE (2020) Kinetics of Loop Closure in Disordered Proteins: Theory vs Simulations
vs Experiments. Journal of Physical Chemistry B. [IF=0.893, Cited=2, 32264681].
- Makarov DE (2021) Barrier Crossing Dynamics from Single-Molecule Measurements. Journal of Physical Chemistry B.
[IF=0.893, Cited=4, 33616401].
- Makarov DE, Hofmann H (2021) Does Electric Friction Matter in Living Cells? Journal of Physical Chemistry B. [IF=0.893,
Cited=2, 34081479].
- Avdoshenko SM, Makarov DE (2015) Reaction Coordinates and Pathways of Mechanochemical Transformations. Journal of
Physical Chemistry B. [IF=0.893, Cited=14, 26401617].
- Avdoshenko SM, Makarov DE (2016) Reply to "Comment on 'Reaction Coordinates and Pathways of Mechanochemical
Transformations'". Journal of Physical Chemistry B. [IF=0.893, Cited=0, 26836974].
- Das A, Makarov DE (2016) Effect of Mutation on an Aggregation-Prone Segment of p53: From Monomer to Dimer to Multimer.
Journal of Physical Chemistry B. [IF=0.893, Cited=4, 27775362].
- Adhikari R, Makarov DE (2017) Mechanochemical Kinetics in Elastomeric Polymer Networks: Heterogeneity of Local Forces
Results in Nonexponential Kinetics. Journal of Physical Chemistry B. [IF=0.893, Cited=6, 28222597].
- Das A, Makarov DE (2018) Dynamics of Disordered Proteins under Confinement: Memory Effects and Internal Friction.
Journal of Physical Chemistry B. [IF=0.893, Cited=4, 30092636].
- Imran A, Moyer BS, Wolfe AJ, ..., Movileanu L (2022) Interplay of Affinity and Surface Tethering in Protein Recognition.
Journal of Physical Chemistry Letters. [IF=1.158, Cited=4, 35485934].
- Berezhkovskii AM, Makarov DE (2018) Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.
Journal of Physical Chemistry Letters. [IF=1.158, Cited=6, 29642698].
- Berezhkovskii AM, Makarov DE (2020) From Nonequilibrium Single-Molecule Trajectories to Underlying Dynamics. Journal of
Physical Chemistry Letters. [IF=1.158, Cited=3, 32017851].
- Uzawa T, Cheng RR, White RJ, ..., Plaxco KW (2010) A mechanistic study of electron transfer from the distal termini of
electrode-bound, single-stranded DNAs. Journal of the American Chemical Society. [IF=2.573, Cited=25, 20964337].
- Watkins HM, Vallée-Bélisle A, Ricci F, ..., Plaxco KW (2012) Entropic and electrostatic effects on the folding free
energy of a surface-attached biomolecule: an experimental and theoretical study. Journal of the American Chemical
Society. [IF=2.573, Cited=20, 22239220].
- Brantley JN, Konda SSM, Makarov DE, Bielawski CW (2012) Regiochemical effects on molecular stability: a mechanochemical
evaluation of 1,4- and 1,5-disubstituted triazoles. Journal of the American Chemical Society. [IF=2.573, Cited=21, 22681196].
- Konda SSM, Brantley JN, Varghese BT, ..., Makarov DE (2013) Molecular catch bonds and the anti-Hammond effect in polymer
mechanochemistry. Journal of the American Chemical Society. [IF=2.573, Cited=36, 23905836].
- Echeverria I, Makarov DE, Papoian GA (2014) Concerted dihedral rotations give rise to internal friction in unfolded
proteins. Journal of the American Chemical Society. [IF=2.573, Cited=49, 24844314].
- Cosa G, Zeng Y, Liu HW, ..., Barbara PF (2006) Evidence for non-two-state kinetics in the nucleocapsid protein
chaperoned opening of DNA hairpins. Journal of Physical Chemistry B. [IF=0.893, Cited=26, 16471833].
- Li PC, Huang L, Makarov DE (2006) Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange
molecular dynamics simulations. Journal of Physical Chemistry B. [IF=0.893, Cited=9, 16854158].
- Huang L, Makarov DE (2007) Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer
chains. Journal of Physical Chemistry A. [IF=0.841, Cited=21, 17637045].
- Cone CW, Cheng RR, Makarov DE, Vanden Bout DA (2011) Molecular weight effect on the formation of β phase
poly(9,9'-dioctylfluorene) in dilute solutions. Journal of Physical Chemistry B. [IF=0.893, Cited=3, 21899310].
- Ting CL, Makarov DE, Wang ZG (2009) A kinetic model for the enzymatic action of cellulase. Journal of Physical Chemistry
B. [IF=0.893, Cited=20, 19292431].
- Cheng RR, Uzawa T, Plaxco KW, Makarov DE (2009) The rate of intramolecular loop formation in DNA and polypeptides: the
absence of the diffusion-controlled limit and fractional power-law viscosity dependence. Journal of Physical Chemistry
B. [IF=0.893, Cited=11, 19780594].
- Cheng RR, Makarov DE (2010) End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide. Journal of
Physical Chemistry B. [IF=0.893, Cited=7, 20151703].
- Sturzenegger F, Zosel F, Holmstrom ED, ..., Schuler B (2018) Transition path times of coupled folding and binding reveal
the formation of an encounter complex. Nature Communications. [IF=3.268, Cited=35, 30413694].
- Avdoshenko SM, Das A, Satija R, ..., Makarov DE (2017) Theoretical and computational validation of the Kuhn barrier
friction mechanism in unfolded proteins. Scientific Reports. [IF=1.312, Cited=8, 28325911].
- Li PC, Makarov DE (2004) Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction
coordinates by changing the pulling geometry. Journal of Chemical Physics. [IF=1.184, Cited=35, 15332917].
- Kirmizialtin S, Huang L, Makarov DE (2005) Topography of the free-energy landscape probed via mechanical unfolding of
proteins. Journal of Chemical Physics. [IF=1.184, Cited=33, 16008495].
- Huang L, Kirmizialtin S, Makarov DE (2005) Computer simulations of the translocation and unfolding of a protein pulled
mechanically through a pore. Journal of Chemical Physics. [IF=1.184, Cited=29, 16392523].
- Huang L, Makarov DE (2006) On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data.
Journal of Chemical Physics. [IF=1.184, Cited=2, 16483197].
- Kirmizialtin S, Makarov DE (2008) Simulations of the untying of molecular friction knots between individual polymer
strands. Journal of Chemical Physics. [IF=1.184, Cited=5, 18331111].
- Ting CL, Makarov DE (2008) Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: a
theoretical study. Journal of Chemical Physics. [IF=1.184, Cited=5, 18361617].
- Huang L, Makarov DE (2008) Translocation of a knotted polypeptide through a pore. Journal of Chemical Physics.
[IF=1.184, Cited=32, 19044999].
- Dickson BM, Makarov DE, Henkelman G (2009) Pitfalls of choosing an order parameter for rare event calculations. Journal
of Chemical Physics. [IF=1.184, Cited=7, 19708733].
- Makarov DE, Plaxco KW (2009) Measuring distances within unfolded biopolymers using fluorescence resonance energy
transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency.
Journal of Chemical Physics. [IF=1.184, Cited=13, 19725638].
- Makarov DE (2010) Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy
transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes. Journal of Chemical Physics.
[IF=1.184, Cited=14, 20095754].
- Chaudhury S, Makarov DE (2010) A harmonic transition state approximation for the duration of reactive events in complex
molecular rearrangements. Journal of Chemical Physics. [IF=1.184, Cited=50, 20649319].
- Cheng RR, Makarov DE (2011) Failure of one-dimensional Smoluchowski diffusion models to describe the duration of
conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization. Journal of
Chemical Physics. [IF=1.184, Cited=16, 21361559].
- Soheilifard R, Makarov DE, Rodin GJ (2011) Rigorous coarse-graining for the dynamics of linear systems with applications
to relaxation dynamics in proteins. Journal of Chemical Physics. [IF=1.184, Cited=4, 21823690].
- Konda SSM, Brantley JN, Bielawski CW, Makarov DE (2011) Chemical reactions modulated by mechanical stress: extended Bell
theory. Journal of Chemical Physics. [IF=1.184, Cited=35, 22047224].
- Makarov DE (2011) The effect of a mechanical force on quantum reaction rate: quantum Bell formula. Journal of Chemical
Physics. [IF=1.184, Cited=5, 22112071].
- Hawk AT, Makarov DE (2011) Milestoning with transition memory. Journal of Chemical Physics. [IF=1.184, Cited=7, 22168682].
- Makarov DE (2013) Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers:
insights from an analytically solvable model. Journal of Chemical Physics. [IF=1.184, Cited=13, 23298023].
- Cheng RR, Hawk AT, Makarov DE (2013) Exploring the role of internal friction in the dynamics of unfolded proteins using
simple polymer models. Journal of Chemical Physics. [IF=1.184, Cited=24, 23445002].
- Hawk AT, Konda SSM, Makarov DE (2013) Computation of transit times using the milestoning method with applications to
polymer translocation. Journal of Chemical Physics. [IF=1.184, Cited=7, 23947837].
- Konda SSM, Avdoshenko SM, Makarov DE (2014) Exploring the topography of the stress-modified energy landscapes of
mechanosensitive molecules. Journal of Chemical Physics. [IF=1.184, Cited=15, 24628159].
- Avdoshenko SM, Konda SSM, Makarov DE (2014) On the calculation of internal forces in mechanically stressed polyatomic
molecules. Journal of Chemical Physics. [IF=1.184, Cited=6, 25296792].
- Makarov DE (2014) Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?
Journal of Chemical Physics. [IF=1.184, Cited=17, 25554124].
- Avdoshenko SM, Makarov DE (2015) Finding mechanochemical pathways and barriers without transition state search. Journal
of Chemical Physics. [IF=1.184, Cited=8, 25956089].
- Makarov DE (2015) Shapes of dominant transition paths from single-molecule force spectroscopy. Journal of Chemical
Physics. [IF=1.184, Cited=15, 26590523].
- Makarov DE (2016) Perspective: Mechanochemistry of biological and synthetic molecules. Journal of Chemical Physics.
[IF=1.184, Cited=25, 26801011].
- Makarov DE (2017) Reconciling transition path time and rate measurements in reactions with large entropic barriers.
Journal of Chemical Physics. [IF=1.184, Cited=14, 28228023].
- Satija R, Das A, Makarov DE (2017) Transition path times reveal memory effects and anomalous diffusion in the dynamics
of protein folding. Journal of Chemical Physics. [IF=1.184, Cited=18, 29055292].
- Berezhkovskii AM, Makarov DE (2017) Communication: Coordinate-dependent diffusivity from single molecule trajectories.
Journal of Chemical Physics. [IF=1.184, Cited=5, 29195291].
- Makarov DE, Schuler B (2018) Preface: Special Topic on Single-Molecule Biophysics. Journal of Chemical Physics.
[IF=1.184, Cited=3, 29604869].
- Berezhkovskii AM, Makarov DE (2018) Communication: Transition-path velocity as an experimental measure of barrier
crossing dynamics. Journal of Chemical Physics. [IF=1.184, Cited=7, 29865813].
- Copperman J, Aristoff D, Makarov DE, ..., Zuckerman DM (2019) Transient probability currents provide upper and lower
bounds on non-equilibrium steady-state currents in the Smoluchowski picture. Journal of Chemical Physics. [IF=1.184,
Cited=3, 31703496].
- Ozmaian M, Makarov DE (2019) Transition path dynamics in the binding of intrinsically disordered proteins: A simulation
study. Journal of Chemical Physics. [IF=1.184, Cited=2, 31864244].
- Berezhkovskii AM, Makarov DE (2020) Detailed balance for diffusion in a potential with trapping and forward-backward
symmetry of trapping time distributions. Journal of Chemical Physics. [IF=1.184, Cited=0, 32534527].
- Berezhkovskii AM, Bezrukov SM, Makarov DE (2021) Localized potential well vs binding site: Mapping solute dynamics in a
membrane channel onto one-dimensional description. Journal of Chemical Physics. [IF=1.184, Cited=1, 33752368].
- Song K, Makarov DE, Vouga E (2023) The effect of time resolution on the observed first passage times in diffusive
dynamics. Journal of Chemical Physics. [IF=1.184, Cited=0, 36948823].
- Song K, Park R, Das A, ..., Vouga E (2023) Non-Markov models of single-molecule dynamics from information-theoretical
analysis of trajectories. Journal of Chemical Physics. [IF=1.184, Cited=1, 37551804].
- Song K, Makarov DE, Vouga E (2024) Information-theoretical limit on the estimates of dissipation by molecular machines
using single-molecule fluorescence resonance energy transfer experiments. Journal of Chemical Physics. [IF=1.184,
Cited=0, 39046347].
- Makarov DE, Keller CA, Plaxco KW, Metiu H (2002) How the folding rate constant of simple, single-domain proteins depends
on the number of native contacts. Proceedings of the National Academy of Sciences of the United States of America.
[IF=2.765, Cited=94, 11904417].
- Soranno A, Buchli B, Nettels D, ..., Schuler B (2012) Quantifying internal friction in unfolded and intrinsically
disordered proteins with single-molecule spectroscopy. Proceedings of the National Academy of Sciences of the United
States of America. [IF=2.765, Cited=162, 22492978].
- Soranno A, Holla A, Dingfelder F, ..., Schuler B (2017) Integrated view of internal friction in unfolded proteins from
single-molecule FRET, contact quenching, theory, and simulations. Proceedings of the National Academy of Sciences of the
United States of America. [IF=2.765, Cited=44, 28223518].
- Satija R, Berezhkovskii AM, Makarov DE (2020) Broad distributions of transition-path times are fingerprints of
multidimensionality of the underlying free energy landscapes. Proceedings of the National Academy of Sciences of the
United States of America. [IF=2.765, Cited=8, 33087575].
- Makarov DE (2021) Life in silico: Are we close yet? Proceedings of the National Academy of Sciences of the United States
of America. [IF=2.765, Cited=1, 33574064].
- Blom K, Song K, Vouga E, ..., Makarov DE (2024) Milestoning estimators of dissipation in systems observed at a coarse
resolution. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=0, 38625949].
- Makri N, Sim E, Makarov DE, Topaler M (1996) Long-time quantum simulation of the primary charge separation in bacterial
photosynthesis. Proceedings of the National Academy of Sciences of the United States of America. [IF=2.765, Cited=24, 8632991].
- Makarov DE (2002) Observation of single molecule transport at surfaces via scanning microscopies: Monte Carlo wave
function study of a model problem. None. [IF=None, Cited=0, 12059564].
- Makarov DE (2009) Comment on "asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling
rates". Physical Review Letters. [IF=2.288, Cited=0, 19392333].
- Zijlstra N, Nettels D, Satija R, ..., Schuler B (2020) Transition Path Dynamics of a Dielectric Particle in a Bistable
Optical Trap. Physical Review Letters. [IF=2.288, Cited=5, 33064519].
- Makarov DE, Plaxco KW (2003) The topomer search model: A simple, quantitative theory of two-state protein folding
kinetics. Protein Science. [IF=1.97, Cited=108, 12493824].
- Ozmaian M, Makarov DE (2023) Long-lived metastable knots in polyampholyte chains. PLoS ONE. [IF=1.253, Cited=1, 37315055].
- Makarov DE (2007) Unraveling individual molecules by mechanical forces: theory meets experiment. Biophysical Journal.
[IF=0.842, Cited=8, 17384065].
- Berezhkovskii AM, Makarov DE (2024) The significance of fuzzy boundaries of the barrier regions in single-molecule
measurements of failed barrier crossing attempts. None. [IF=None, Cited=0, 38903733].
Publication with MISSING institution:
- Wang Z, Plaxco KW, Makarov DE (2007) Influence of local and residual structures on the scaling behavior and dimensions
of unfolded proteins. Biopolymers. [IF=0.522, Cited=24, 17450572].
- Madsen JA, Cheng RR, Kaoud TS, ..., Brodbelt JS (2012) Charge-site-dependent dissociation of hydrogen-rich radical
peptide cations upon vacuum UV photoexcitation. Chemistry - A European Journal. [IF=0.899, Cited=15, 22431222].
- Uzawa T, Cheng RR, Cash KJ, ..., Plaxco KW (2009) The length and viscosity dependence of end-to-end collision rates in
single-stranded DNA. Biophysical Journal. [IF=0.842, Cited=15, 19580758].
- Taylor JN, Makarov DE, Landes CF (2010) Denoising single-molecule FRET trajectories with wavelets and Bayesian
inference. Biophysical Journal. [IF=0.842, Cited=25, 20074517].
- Cheng RR, Uzawa T, Plaxco KW, Makarov DE (2010) Universality in the timescales of internal loop formation in unfolded
proteins and single-stranded oligonucleotides. Biophysical Journal. [IF=0.842, Cited=10, 21156138].
- Uzawa T, Isoshima T, Ito Y, ..., Plaxco KW (2013) Sequence and temperature dependence of the end-to-end collision
dynamics of single-stranded DNA. Biophysical Journal. [IF=0.842, Cited=6, 23746521].
- McCarney ER, Werner JH, Bernstein SL, ..., Plaxco KW (2005) Site-specific dimensions across a highly denatured protein;
a single molecule study. Journal of Molecular Biology. [IF=1.281, Cited=44, 16095607].
- Makarov DE, Berezhkovskii A, Haran G, Pollak E (2022) The Effect of Time Resolution on Apparent Transition Path Times
Observed in Single-Molecule Studies of Biomolecules. Journal of Physical Chemistry B. [IF=0.893, Cited=1, 36194758].
- Medina E, Satija R, Makarov DE (2018) Transition Path Times in Non-Markovian Activated Rate Processes. Journal of
Physical Chemistry B. [IF=0.893, Cited=6, 30179506].
- Satija R, Makarov DE (2019) Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular
Folding. Journal of Physical Chemistry B. [IF=0.893, Cited=5, 30648875].
- Godec A, Makarov DE (2022) Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule
Fluorescence Resonance Energy Transfer Trajectories. Journal of Physical Chemistry Letters. [IF=1.158, Cited=3, 36566432].
- Becker N, Oroudjev E, Mutz S, ..., Hansma HG (2003) Molecular nanosprings in spider capture-silk threads. Nature
Materials. [IF=6.645, Cited=125, 12690403].
- Soheilifard R, Makarov DE, Rodin GJ (2008) Critical evaluation of simple network models of protein dynamics and their
comparison with crystallographic B-factors. Physical Biology. [IF=0.648, Cited=26, 18577808].
- Eom K, Makarov DE, Rodin GJ (2005) Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer
chains and their implications for single-molecule pulling experiments. None. [IF=None, Cited=9, 15783349].