| Year |
Citation |
Score |
| 2023 |
Song K, Park R, Das A, Makarov DE, Vouga E. Non-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories. The Journal of Chemical Physics. 159. PMID 37551804 DOI: 10.1063/5.0158930 |
0.656 |
|
| 2022 |
Makarov DE, Berezhkovskii A, Haran G, Pollak E. The Effect of Time Resolution on Apparent Transition Path Times Observed in Single-Molecule Studies of Biomolecules. The Journal of Physical Chemistry. B. PMID 36194758 DOI: 10.1021/acs.jpcb.2c05550 |
0.315 |
|
| 2020 |
Satija R, Berezhkovskii AM, Makarov DE. 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. PMID 33087575 DOI: 10.1073/pnas.2008307117 |
0.309 |
|
| 2020 |
Ma P, Elber R, Makarov DE. The value of temporal information when analyzing reaction coordinates. Journal of Chemical Theory and Computation. PMID 32841001 DOI: 10.1021/Acs.Jctc.0C00678 |
0.311 |
|
| 2020 |
Satija R, Das A, Mühle S, Enderlein J, Makarov DE. Kinetics of Loop Closure in Disordered Proteins: Theory vs Simulations vs Experiments. The Journal of Physical Chemistry. B. PMID 32264681 DOI: 10.1021/Acs.Jpcb.0C01437 |
0.699 |
|
| 2020 |
Berezhkovskii AM, Makarov DE. From Nonequilibrium Single-Molecules Trajectories to Underlying Dynamics. The Journal of Physical Chemistry Letters. PMID 32017851 DOI: 10.1021/Acs.Jpclett.9B03705 |
0.397 |
|
| 2019 |
Ozmaian M, Makarov DE. Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study. The Journal of Chemical Physics. 151: 235101. PMID 31864244 DOI: 10.1063/1.5129150 |
0.445 |
|
| 2019 |
Copperman J, Aristoff D, Makarov DE, Simpson G, Zuckerman DM. Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture. The Journal of Chemical Physics. 151: 174108. PMID 31703496 DOI: 10.1063/1.5120511 |
0.33 |
|
| 2019 |
Renn JP, Bhattacharyya S, Bai H, He C, Li H, Oberhauser AF, Marko JF, Makarov DE, Matouschek A. Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force. Scientific Reports. 9: 11101. PMID 31366931 DOI: 10.1038/S41598-019-46525-W |
0.358 |
|
| 2019 |
Satija R, Makarov DE. Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding. The Journal of Physical Chemistry. B. 123: 802-810. PMID 30648875 DOI: 10.1021/Acs.Jpcb.8B11137 |
0.373 |
|
| 2019 |
Satija R, Makarov DE. Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding. The Journal of Physical Chemistry. A. PMID 30605332 DOI: 10.1021/Acs.Jpca.8B11137 |
0.373 |
|
| 2019 |
Berezhkovskii AM, Makarov DE. On the forward/backward symmetry of transition path time distributions in nonequilibrium systems The Journal of Chemical Physics. 151: 065102. DOI: 10.1063/1.5109293 |
0.379 |
|
| 2018 |
Sturzenegger F, Zosel F, Holmstrom ED, Buholzer KJ, Makarov DE, Nettels D, Schuler B. Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nature Communications. 9: 4708. PMID 30413694 DOI: 10.1038/S41467-018-07043-X |
0.353 |
|
| 2018 |
Medina E, Satija R, Makarov DE. Transition Path Times In Non-Markovian Activated Rate Processes. The Journal of Physical Chemistry. B. PMID 30179506 DOI: 10.1021/Acs.Jpcb.8B07361 |
0.393 |
|
| 2018 |
Das A, Makarov DE. Dynamics of Disordered Proteins Under Confinement: Memory Effects and Internal Friction. The Journal of Physical Chemistry. B. PMID 30092636 DOI: 10.1021/Acs.Jpcb.8B06112 |
0.715 |
|
| 2018 |
Berezhkovskii AM, Makarov DE. Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics. The Journal of Chemical Physics. 148: 201102. PMID 29865813 DOI: 10.1063/1.5030427 |
0.38 |
|
| 2018 |
Berezhkovskii AM, Makarov DE. Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate. The Journal of Physical Chemistry Letters. 2190-2195. PMID 29642698 DOI: 10.1021/Acs.Jpclett.8B00956 |
0.364 |
|
| 2018 |
Makarov DE, Schuler B. Preface: Special Topic on Single-Molecule Biophysics. The Journal of Chemical Physics. 148: 123001. PMID 29604869 DOI: 10.1063/1.5028275 |
0.307 |
|
| 2018 |
Dauphin-Ducharme P, Arroyo-Currás N, Adhikari R, Somerson J, Ortega G, Makarov DE, Plaxco KW. Chain Dynamics Limit Electron Transfer from Electrode-Bound, Single-Stranded Oligonucleotides The Journal of Physical Chemistry C. 122: 21441-21448. DOI: 10.1021/Acs.Jpcc.8B06111 |
0.359 |
|
| 2017 |
Berezhkovskii AM, Makarov DE. Communication: Coordinate-dependent diffusivity from single molecule trajectories. The Journal of Chemical Physics. 147: 201102. PMID 29195291 DOI: 10.1063/1.5006456 |
0.352 |
|
| 2017 |
Satija R, Das A, Makarov DE. Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding. The Journal of Chemical Physics. 147: 152707. PMID 29055292 DOI: 10.1063/1.4993228 |
0.7 |
|
| 2017 |
Avdoshenko SM, Das A, Satija R, Papoian GA, Makarov DE. Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins. Scientific Reports. 7: 269. PMID 28325911 DOI: 10.1038/S41598-017-00287-5 |
0.708 |
|
| 2017 |
Makarov DE. Reconciling transition path time and rate measurements in reactions with large entropic barriers. The Journal of Chemical Physics. 146: 071101. PMID 28228023 DOI: 10.1063/1.4977177 |
0.412 |
|
| 2017 |
Soranno A, Holla A, Dingfelder F, Nettels D, Makarov DE, Schuler B. 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. PMID 28223518 DOI: 10.1073/Pnas.1616672114 |
0.468 |
|
| 2017 |
Adhikari R, Makarov DE. Mechanochemical Kinetics in Elastomeric Polymer Networks: Heterogeneity of Local Forces Results in Nonexponential Kinetics. The Journal of Physical Chemistry. B. PMID 28222597 DOI: 10.1021/Acs.Jpcb.6B12758 |
0.369 |
|
| 2016 |
Das A, Makarov DE. Effect of Mutation on an Aggregation-Prone Segment of p53: From Monomer to Dimer to Multimer. The Journal of Physical Chemistry. B. PMID 27775362 DOI: 10.1021/Acs.Jpcb.6B07457 |
0.624 |
|
| 2016 |
Makarov DE. Perspective: Mechanochemistry of biological and synthetic molecules. The Journal of Chemical Physics. 144: 030901. PMID 26801011 DOI: 10.1063/1.4939791 |
0.392 |
|
| 2016 |
Nam GM, Makarov DE. Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments. Protein Science : a Publication of the Protein Society. 25: 123-34. PMID 26088347 DOI: 10.1002/Pro.2727 |
0.418 |
|
| 2015 |
Makarov DE. Shapes of dominant transition paths from single-molecule force spectroscopy. The Journal of Chemical Physics. 143: 194103. PMID 26590523 DOI: 10.1063/1.4935706 |
0.365 |
|
| 2015 |
Avdoshenko SM, Makarov DE. Finding mechanochemical pathways and barriers without transition state search. The Journal of Chemical Physics. 142: 174106. PMID 25956089 DOI: 10.1063/1.4919541 |
0.359 |
|
| 2014 |
Makarov DE. Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties? The Journal of Chemical Physics. 141: 241103. PMID 25554124 DOI: 10.1063/1.4904895 |
0.388 |
|
| 2014 |
Avdoshenko SM, Konda SS, Makarov DE. On the calculation of internal forces in mechanically stressed polyatomic molecules. The Journal of Chemical Physics. 141: 134115. PMID 25296792 DOI: 10.1063/1.4896944 |
0.332 |
|
| 2014 |
Echeverria I, Makarov DE, Papoian GA. Concerted dihedral rotations give rise to internal friction in unfolded proteins. Journal of the American Chemical Society. 136: 8708-13. PMID 24844314 DOI: 10.1021/Ja503069K |
0.45 |
|
| 2014 |
Konda SS, Avdoshenko SM, Makarov DE. Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules. The Journal of Chemical Physics. 140: 104114. PMID 24628159 DOI: 10.1063/1.4867500 |
0.351 |
|
| 2014 |
Makarov DE. Computational and theoretical insights into protein and peptide translocation. Protein and Peptide Letters. 21: 217-26. PMID 24370258 DOI: 10.2174/09298665113209990073 |
0.368 |
|
| 2013 |
Levy RM, Dai W, Deng NJ, Makarov DE. How long does it take to equilibrate the unfolded state of a protein? Protein Science : a Publication of the Protein Society. 22: 1459-65. PMID 23963761 DOI: 10.1002/Pro.2335 |
0.33 |
|
| 2013 |
Hawk AT, Konda SS, Makarov DE. Computation of transit times using the milestoning method with applications to polymer translocation. The Journal of Chemical Physics. 139: 064101. PMID 23947837 DOI: 10.1063/1.4817200 |
0.416 |
|
| 2013 |
Konda SS, Brantley JN, Varghese BT, Wiggins KM, Bielawski CW, Makarov DE. Molecular catch bonds and the anti-Hammond effect in polymer mechanochemistry. Journal of the American Chemical Society. 135: 12722-9. PMID 23905836 DOI: 10.1021/Ja4051108 |
0.375 |
|
| 2013 |
Uzawa T, Isoshima T, Ito Y, Ishimori K, Makarov DE, Plaxco KW. Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA. Biophysical Journal. 104: 2485-92. PMID 23746521 DOI: 10.1016/J.Bpj.2013.03.053 |
0.373 |
|
| 2013 |
Cheng RR, Hawk AT, Makarov DE. Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models. The Journal of Chemical Physics. 138: 074112. PMID 23445002 DOI: 10.1063/1.4792206 |
0.766 |
|
| 2013 |
Makarov DE. Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: insights from an analytically solvable model. The Journal of Chemical Physics. 138: 014102. PMID 23298023 DOI: 10.1063/1.4773283 |
0.413 |
|
| 2013 |
Echeverria I, Makarov DE, Papoian G. Insight into the Molecular Origins of the Internal Friction in Unfolded Proteins Biophysical Journal. 104: 188a. DOI: 10.1016/J.Bpj.2012.11.1061 |
0.467 |
|
| 2012 |
Brantley JN, Konda SS, Makarov DE, Bielawski CW. Regiochemical effects on molecular stability: a mechanochemical evaluation of 1,4- and 1,5-disubstituted triazoles. Journal of the American Chemical Society. 134: 9882-5. PMID 22681196 DOI: 10.1021/Ja303147A |
0.376 |
|
| 2012 |
Soranno A, Buchli B, Nettels D, Cheng RR, Müller-Späth S, Pfeil SH, Hoffmann A, Lipman EA, Makarov DE, Schuler B. 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. 109: 17800-6. PMID 22492978 DOI: 10.1073/Pnas.1117368109 |
0.764 |
|
| 2012 |
Madsen JA, Cheng RR, Kaoud TS, Dalby KN, Makarov DE, Brodbelt JS. Charge-site-dependent dissociation of hydrogen-rich radical peptide cations upon vacuum UV photoexcitation. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 5374-83. PMID 22431222 DOI: 10.1002/Chem.201103534 |
0.707 |
|
| 2012 |
Watkins HM, Vallée-Bélisle A, Ricci F, Makarov DE, Plaxco KW. 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. 134: 2120-6. PMID 22239220 DOI: 10.1021/Ja208436P |
0.329 |
|
| 2011 |
Hawk AT, Makarov DE. Milestoning with transition memory. The Journal of Chemical Physics. 135: 224109. PMID 22168682 DOI: 10.1063/1.3666840 |
0.373 |
|
| 2011 |
Makarov DE. The effect of a mechanical force on quantum reaction rate: quantum Bell formula. The Journal of Chemical Physics. 135: 194112. PMID 22112071 DOI: 10.1063/1.3661157 |
0.355 |
|
| 2011 |
Konda SS, Brantley JN, Bielawski CW, Makarov DE. Chemical reactions modulated by mechanical stress: extended Bell theory. The Journal of Chemical Physics. 135: 164103. PMID 22047224 DOI: 10.1063/1.3656367 |
0.339 |
|
| 2011 |
Cone CW, Cheng RR, Makarov DE, Vanden Bout DA. Molecular weight effect on the formation of β phase poly(9,9'-dioctylfluorene) in dilute solutions. The Journal of Physical Chemistry. B. 115: 12380-5. PMID 21899310 DOI: 10.1021/Jp2061078 |
0.707 |
|
| 2011 |
Soheilifard R, Makarov DE, Rodin GJ. Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins. The Journal of Chemical Physics. 135: 054107. PMID 21823690 DOI: 10.1063/1.3613678 |
0.368 |
|
| 2011 |
Cheng RR, Makarov DE. 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. The Journal of Chemical Physics. 134: 085104. PMID 21361559 DOI: 10.1063/1.3556750 |
0.756 |
|
| 2010 |
Cheng RR, Uzawa T, Plaxco KW, Makarov DE. Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophysical Journal. 99: 3959-68. PMID 21156138 DOI: 10.1016/J.Bpj.2010.11.017 |
0.757 |
|
| 2010 |
Lu CY, Makarov DE, Henkelman G. Communication: κ-dynamics--an exact method for accelerating rare event classical molecular dynamics. The Journal of Chemical Physics. 133: 201101. PMID 21133434 DOI: 10.1063/1.3514030 |
0.343 |
|
| 2010 |
Uzawa T, Cheng RR, White RJ, Makarov DE, Plaxco KW. A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs. Journal of the American Chemical Society. 132: 16120-6. PMID 20964337 DOI: 10.1021/Ja106345D |
0.718 |
|
| 2010 |
Chaudhury S, Makarov DE. A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements. The Journal of Chemical Physics. 133: 034118. PMID 20649319 DOI: 10.1063/1.3459058 |
0.348 |
|
| 2010 |
Cheng RR, Makarov DE. End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide. The Journal of Physical Chemistry. B. 114: 3321-9. PMID 20151703 DOI: 10.1021/Jp910669D |
0.724 |
|
| 2010 |
Makarov DE. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes. The Journal of Chemical Physics. 132: 035104. PMID 20095754 DOI: 10.1063/1.3284509 |
0.375 |
|
| 2010 |
Taylor JN, Makarov DE, Landes CF. Denoising single-molecule FRET trajectories with wavelets and Bayesian inference. Biophysical Journal. 98: 164-73. PMID 20074517 DOI: 10.1016/J.Bpj.2009.09.047 |
0.317 |
|
| 2010 |
Uzawa T, Ishimori K, Makarov DE, Plaxco KW. 2P133 Simple polymer physics underlying the end-to-end collision dynamics of single-stranded DNA(The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50: S105. DOI: 10.2142/Biophys.50.S105_5 |
0.32 |
|
| 2010 |
Landes CF, Taylor JN, Makarov DE. De-Noising Single Molecule FRET Trajectories using Wavelent and Bayesian Techniques Biophysical Journal. 98: 589a. DOI: 10.1016/J.Bpj.2009.12.3205 |
0.303 |
|
| 2009 |
Cheng RR, Uzawa T, Plaxco KW, Makarov DE. The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence. The Journal of Physical Chemistry. B. 113: 14026-34. PMID 19780594 DOI: 10.1021/Jp902291N |
0.75 |
|
| 2009 |
Makarov DE, Plaxco KW. Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency. The Journal of Chemical Physics. 131: 085105. PMID 19725638 DOI: 10.1063/1.3212602 |
0.362 |
|
| 2009 |
Dickson BM, Makarov DE, Henkelman G. Pitfalls of choosing an order parameter for rare event calculations. The Journal of Chemical Physics. 131: 074108. PMID 19708733 DOI: 10.1063/1.3204008 |
0.312 |
|
| 2009 |
Uzawa T, Cheng RR, Cash KJ, Makarov DE, Plaxco KW. The length and viscosity dependence of end-to-end collision rates in single-stranded DNA. Biophysical Journal. 97: 205-10. PMID 19580758 DOI: 10.1016/J.Bpj.2009.04.036 |
0.752 |
|
| 2009 |
Ting CL, Makarov DE, Wang ZG. A kinetic model for the enzymatic action of cellulase. The Journal of Physical Chemistry. B. 113: 4970-7. PMID 19292431 DOI: 10.1021/Jp810625K |
0.356 |
|
| 2009 |
Makarov DE. A theoretical model for the mechanical unfolding of repeat proteins. Biophysical Journal. 96: 2160-7. PMID 19289042 DOI: 10.1016/J.Bpj.2008.12.3899 |
0.389 |
|
| 2009 |
Makarov DE. Computer simulations and theory of protein translocation. Accounts of Chemical Research. 42: 281-9. PMID 19072704 DOI: 10.1021/Ar800128X |
0.398 |
|
| 2008 |
Huang L, Makarov DE. Translocation of a knotted polypeptide through a pore. The Journal of Chemical Physics. 129: 121107. PMID 19044999 DOI: 10.1063/1.2968554 |
0.399 |
|
| 2008 |
Soheilifard R, Makarov DE, Rodin GJ. Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors. Physical Biology. 5: 026008. PMID 18577808 DOI: 10.1088/1478-3975/5/2/026008 |
0.35 |
|
| 2008 |
Ting CL, Makarov DE. Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: a theoretical study. The Journal of Chemical Physics. 128: 115102. PMID 18361617 DOI: 10.1063/1.2835611 |
0.394 |
|
| 2008 |
Huang L, Makarov DE. The rate constant of polymer reversal inside a pore. The Journal of Chemical Physics. 128: 114903. PMID 18361614 DOI: 10.1063/1.2890006 |
0.39 |
|
| 2008 |
Kirmizialtin S, Makarov DE. Simulations of the untying of molecular friction knots between individual polymer strands. The Journal of Chemical Physics. 128: 094901. PMID 18331111 DOI: 10.1063/1.2835605 |
0.695 |
|
| 2007 |
Huang L, Makarov DE. Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains. The Journal of Physical Chemistry. A. 111: 10338-44. PMID 17637045 DOI: 10.1021/Jp071940+ |
0.39 |
|
| 2007 |
Wang Z, Plaxco KW, Makarov DE. Influence of local and residual structures on the scaling behavior and dimensions of unfolded proteins. Biopolymers. 86: 321-8. PMID 17450572 DOI: 10.1002/Bip.20747 |
0.339 |
|
| 2007 |
Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov DE, Movileanu L. Single-molecule electrophoresis of beta-hairpin peptides by electrical recordings and Langevin dynamics simulations. The Journal of Physical Chemistry. B. 111: 3332-5. PMID 17388500 DOI: 10.1021/Jp071364H |
0.661 |
|
| 2007 |
Makarov DE. Unraveling individual molecules by mechanical forces: theory meets experiment. Biophysical Journal. 92: 4135-6. PMID 17384065 DOI: 10.1529/Biophysj.107.105650 |
0.352 |
|
| 2006 |
Li PC, Huang L, Makarov DE. Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange molecular dynamics simulations. The Journal of Physical Chemistry. B. 110: 14469-74. PMID 16854158 DOI: 10.1021/Jp056422I |
0.59 |
|
| 2006 |
Cosa G, Zeng Y, Liu HW, Landes CF, Makarov DE, Musier-Forsyth K, Barbara PF. Evidence for non-two-state kinetics in the nucleocapsid protein chaperoned opening of DNA hairpins. The Journal of Physical Chemistry. B. 110: 2419-26. PMID 16471833 DOI: 10.1021/Jp054189I |
0.377 |
|
| 2006 |
Kirmizialtin S, Huang L, Makarov DE. Computer simulations of protein translocation Physica Status Solidi (B) Basic Research. 243: 2038-2047. DOI: 10.1002/Pssb.200666812 |
0.7 |
|
| 2005 |
Huang L, Kirmizialtin S, Makarov DE. Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore. The Journal of Chemical Physics. 123: 124903. PMID 16392523 DOI: 10.1063/1.2008231 |
0.715 |
|
| 2005 |
McCarney ER, Werner JH, Bernstein SL, Ruczinski I, Makarov DE, Goodwin PM, Plaxco KW. Site-specific dimensions across a highly denatured protein; a single molecule study. Journal of Molecular Biology. 352: 672-82. PMID 16095607 DOI: 10.1016/J.Jmb.2005.07.015 |
0.368 |
|
| 2005 |
Kirmizialtin S, Huang L, Makarov DE. Topography of the free-energy landscape probed via mechanical unfolding of proteins. The Journal of Chemical Physics. 122: 234915. PMID 16008495 DOI: 10.1063/1.1931659 |
0.705 |
|
| 2005 |
Eom K, Makarov DE, Rodin GJ. Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single-molecule pulling experiments. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 021904. PMID 15783349 DOI: 10.1103/Physreve.71.021904 |
0.368 |
|
| 2004 |
Kirmizialtin S, Ganesan V, Makarov DE. Translocation of a beta-hairpin-forming peptide through a cylindrical tunnel. The Journal of Chemical Physics. 121: 10268-77. PMID 15549903 DOI: 10.1063/1.1807832 |
0.672 |
|
| 2004 |
Li PC, Makarov DE. Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction coordinates by changing the pulling geometry. The Journal of Chemical Physics. 121: 4826-32. PMID 15332917 DOI: 10.1063/1.1778152 |
0.549 |
|
| 2004 |
Li P, Makarov DE. Ubiquitin-like Protein Domains Show High Resistance to Mechanical Unfolding Similar to That of the I27 Domain in Titin: Evidence from Simulations The Journal of Physical Chemistry B. 108: 745-749. DOI: 10.1021/Jp0363895 |
0.585 |
|
| 2003 |
Becker N, Oroudjev E, Mutz S, Cleveland JP, Hansma PK, Hayashi CY, Makarov DE, Hansma HG. Molecular nanosprings in spider capture-silk threads. Nature Materials. 2: 278-83. PMID 12690403 DOI: 10.1038/Nmat858 |
0.352 |
|
| 2003 |
Makarov DE, Plaxco KW. The topomer search model: A simple, quantitative theory of two-state protein folding kinetics. Protein Science : a Publication of the Protein Society. 12: 17-26. PMID 12493824 DOI: 10.1110/Ps.0220003 |
0.411 |
|
| 2003 |
Li P, Makarov DE. Theoretical studies of the mechanical unfolding of the muscle protein titin: Bridging the time-scale gap between simulation and experiment The Journal of Chemical Physics. 119: 9260-9268. DOI: 10.1063/1.1615233 |
0.589 |
|
| 2003 |
Makarov DE, Wang Z, Hansma HG. Response to “Comment on ‘On the interpretation of force-extension curves of single protein molecules’ ” [J. Chem. Phys. 118, 2964 (2003)] The Journal of Chemical Physics. 118: 2966. DOI: 10.1063/1.1535895 |
0.361 |
|
| 2003 |
Eom K, Li P, Makarov DE, Rodin GJ. Relationship between the Mechanical Properties and Topology of Cross-Linked Polymer Molecules: Parallel Strands Maximize the Strength of Model Polymers and Protein Domains The Journal of Physical Chemistry B. 107: 8730-8733. DOI: 10.1021/Jp035178X |
0.372 |
|
| 2003 |
Wang Z, Makarov DE. Nanosecond Dynamics of Single Polypeptide Molecules Revealed by Photoemission Statistics of Fluorescence Resonance Energy Transfer: A Theoretical Study The Journal of Physical Chemistry B. 107: 5617-5622. DOI: 10.1021/Jp034285O |
0.373 |
|
| 2002 |
Makarov DE, Rodin GJ. Configurational entropy and mechanical properties of cross-linked polymer chains: implications for protein and RNA folding. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 66: 011908. PMID 12241385 DOI: 10.1103/Physreve.66.011908 |
0.388 |
|
| 2002 |
Makarov DE. Observation of single molecule transport at surfaces via scanning microscopies: Monte Carlo wave function study of a model problem. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 051601. PMID 12059564 DOI: 10.1103/Physreve.65.051601 |
0.326 |
|
| 2002 |
Makarov DE, Keller CA, Plaxco KW, Metiu H. 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. 99: 3535-9. PMID 11904417 DOI: 10.1073/Pnas.052713599 |
0.549 |
|
| 2002 |
Wang Z, Makarov DE. Rate of intramolecular contact formation in peptides: The loop length dependence The Journal of Chemical Physics. 117: 4591-4593. DOI: 10.1063/1.1497638 |
0.342 |
|
| 2002 |
Makarov DE, Wang Z, Thompson JB, Hansma HG. On the interpretation of force extension curves of single protein molecules The Journal of Chemical Physics. 116: 7760-7765. DOI: 10.1063/1.1466835 |
0.361 |
|
| 2002 |
Makarov DE, Metiu H. A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results The Journal of Chemical Physics. 116: 5205. DOI: 10.1063/1.1450123 |
0.575 |
|
| 2001 |
Makarov DE, Metiu H. Control, with a rf field, of photon emission times by a single molecule and its connection to laser-induced localization of an electron in a double well The Journal of Chemical Physics. 115: 5989-5993. DOI: 10.1063/1.1392377 |
0.477 |
|
| 2001 |
Makarov DE, Hansma PK, Metiu H. Kinetic Monte Carlo simulation of titin unfolding Journal of Chemical Physics. 114: 9663-9673. DOI: 10.1063/1.1369622 |
0.557 |
|
| 1999 |
Makarov DE, Metiu H. Quantum dynamics with dissipation: A treatment of dephasing in the stochastic Schrödinger equation The Journal of Chemical Physics. 111: 10126-10136. DOI: 10.1063/1.480390 |
0.469 |
|
| 1999 |
Makarov DE, Metiu H. Stochastic Schrödinger equation. II. A study of the coherence seen in pump-probe experiments that use a strong pump laser The Journal of Chemical Physics. 111: 10137-10147. DOI: 10.1063/1.480364 |
0.506 |
|
| 1998 |
Makarov DE, Metiu H. Some constraints involving the statistical properties of trajectories run in the Monte Carlo computation of a rate constant and their use in improving and testing the quality of sampling The Journal of Chemical Physics. 108: 8155-8160. DOI: 10.1063/1.476170 |
0.526 |
|
| 1998 |
Makarov DE, Metiu H. Fitting potential-energy surfaces: A search in the function space by directed genetic programming The Journal of Chemical Physics. 108: 590-598. DOI: 10.1063/1.475421 |
0.448 |
|
| 1997 |
Makarov DE, Metiu H. The reaction rate constant in a system with localized trajectories in the transition region: Classical and quantum dynamics The Journal of Chemical Physics. 107: 7787-7799. DOI: 10.1063/1.475092 |
0.55 |
|
| 1997 |
Mills G, Schenter G, Makarov D, Jónsson H. Generalized path integral based quantum transition state theory Chemical Physics Letters. 278: 91-96. DOI: 10.1016/S0009-2614(97)00886-5 |
0.316 |
|
| 1996 |
Makri N, Sim E, Makarov DE, Topaler M. 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. 93: 3926-31. PMID 8632991 DOI: 10.1073/Pnas.93.9.3926 |
0.602 |
|
| 1995 |
Makarov DE, Makri N. Stochastic resonance and nonlinear response in double-quantum-well structures. Physical Review. B, Condensed Matter. 52: R2257-R2260. PMID 9981385 DOI: 10.1103/Physrevb.52.R2257 |
0.528 |
|
| 1995 |
Makarov DE, Makri N. Control of dissipative tunneling dynamics by continuous wave electromagnetic fields: Localization and large-amplitude coherent motion. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 52: 5863-5872. PMID 9964101 DOI: 10.1103/Physreve.52.5863 |
0.545 |
|
| 1995 |
Makarov DE, Topaler M. Quantum transition-state theory below the crossover temperature. Physical Review E. 52: 178-188. PMID 9963418 DOI: 10.1103/Physreve.52.178 |
0.312 |
|
| 1995 |
Makri N, Makarov DE. Tensor propagator for iterative quantum time evolution of reduced density matrices. II. Numerical methodology The Journal of Chemical Physics. 102: 4611-4618. DOI: 10.1063/1.469509 |
0.591 |
|
| 1995 |
Makri N, Makarov DE. Tensor propagator for iterative quantum time evolution of reduced density matrices. I. Theory The Journal of Chemical Physics. 102: 4600-4610. DOI: 10.1063/1.469508 |
0.594 |
|
| 1994 |
Benderskii VA, Grebenshchikov SY, Vetoshkin EV, Mil'nikov GV, Makarov DE. Two-Dimensional Tunneling: Bifurcations and Competing Trajectories The Journal of Physical Chemistry. 98: 3300-3306. DOI: 10.1021/J100064A010 |
0.311 |
|
| 1994 |
Benderskii V, Grebenshchikov S, Makarov D, Vetoshkin E. Tunneling trajectories of two-proton transfer Chemical Physics. 185: 101-112. DOI: 10.1016/0301-0104(94)00092-1 |
0.335 |
|
| 1994 |
Makarov DE, Makri N. Path integrals for dissipative systems by tensor multiplication. Condensed phase quantum dynamics for arbitrarily long time Chemical Physics Letters. 221: 482-491. DOI: 10.1016/0009-2614(94)00275-4 |
0.584 |
|
| 1993 |
Makarov DE, Makri N. Tunneling dynamics in dissipative curve-crossing problems. Physical Review. A. 48: 3626-3635. PMID 9910029 DOI: 10.1103/Physreva.48.3626 |
0.606 |
|
| 1993 |
Benderskii V, Goldanskii V, Makarov D. Quantum dynamics in low-temperature chemistry Physics Reports. 233: 195-339. DOI: 10.1016/0370-1573(93)90136-2 |
0.372 |
|
| 1992 |
Benderskii V, Makarov D, Pastur D, Grinevich P. Preexponential factor of the rate constant of low-temperature chemical reactions. Fluctuational width of tunneling channels and stability frequencies Chemical Physics. 161: 51-61. DOI: 10.1016/0301-0104(92)80176-V |
0.323 |
|
| 1991 |
Benderskii V, Goldanskii V, Makarov D, Misochko E. Dynamics of multidimensional nuclear tunneling in the chain-ethylene chlorination at liquid-helium temperature Chemical Physics Letters. 179: 334-338. DOI: 10.1016/0009-2614(91)85162-P |
0.339 |
|
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