All Stories

  1. Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states

    Article • The Journal of Chemical Physics, January 2025, American Institute of Physics

    Dmitrii Makarov, Anatoly Kolomeisky

  2. The significance of fuzzy boundaries of the barrier regions in single-molecule measurements of failed barrier crossing attempts

    Article • The Journal of Chemical Physics, September 2024, American Institute of Physics

    Dmitrii Makarov

  3. Information-theoretical limit on the estimates of dissipation by molecular machines using single-molecule fluorescence resonance energy transfer experiments

    Article • The Journal of Chemical Physics, July 2024, American Institute of Physics

    Dmitrii Makarov

  4. Milestoning estimators of dissipation in systems observed at a coarse resolution

    Article • Proceedings of the National Academy of Sciences, April 2024, Proceedings of the National Academy of Sciences

    Dmitrii Makarov

  5. The effect of time resolution on the observed first passage times in diffusive dynamics

    Article • The Journal of Chemical Physics, March 2023, American Institute of Physics

    Dmitrii Makarov

  6. Localized potential well vs binding site: Mapping solute dynamics in a membrane channel onto one-dimensional description

    Article • The Journal of Chemical Physics, March 2021, American Institute of Physics

    Dmitrii Makarov

  7. Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes

    Article • Proceedings of the National Academy of Sciences, October 2020, Proceedings of the National Academy of Sciences

    Dmitrii Makarov

  8. Detailed balance for diffusion in a potential with trapping and forward–backward symmetry of trapping time distributions

    Article • The Journal of Chemical Physics, June 2020, American Institute of Physics

    Dmitrii Makarov

  9. Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study

    Article • The Journal of Chemical Physics, December 2019, American Institute of Physics

    Dmitrii Makarov

  10. Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture

    Article • The Journal of Chemical Physics, November 2019, American Institute of Physics

    Dmitrii Makarov

  11. On the forward/backward symmetry of transition path time distributions in nonequilibrium systems

    Article • The Journal of Chemical Physics, August 2019, American Institute of Physics

    Dmitrii Makarov

  12. Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins

    Article • Journal of the American Chemical Society, June 2014, American Chemical Society (ACS)

    Dmitrii Makarov

  13. Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules

    Article • The Journal of Chemical Physics, March 2014, American Institute of Physics

    Dmitrii Makarov

  14. Computational and Theoretical Insights into Protein and Peptide Translocation

    Article • Protein and Peptide Letters, January 2014, Bentham Science Publishers

    Dmitrii Makarov

  15. How long does it take to equilibrate the unfolded state of a protein?

    Article • Protein Science, September 2013, Wiley

    Dmitrii Makarov

  16. Molecular Catch Bonds and the Anti-Hammond Effect in Polymer Mechanochemistry

    Article • Journal of the American Chemical Society, August 2013, American Chemical Society (ACS)

    Dmitrii Makarov

  17. Computation of transit times using the milestoning method with applications to polymer translocation

    Article • The Journal of Chemical Physics, August 2013, American Institute of Physics

    Dmitrii Makarov

  18. Sequence and Temperature Dependence of the End-to-End Collision Dynamics of Single-Stranded DNA

    Article • Biophysical Journal, June 2013, Elsevier

    Dmitrii Makarov

  19. Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

    Article • The Journal of Chemical Physics, February 2013, American Institute of Physics

    Dmitrii Makarov

  20. Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: Insights from an analytically solvable model

    Article • The Journal of Chemical Physics, January 2013, American Institute of Physics

    Dmitrii Makarov

  21. Regiochemical Effects on Molecular Stability: A Mechanochemical Evaluation of 1,4- and 1,5-Disubstituted Triazoles

    Article • Journal of the American Chemical Society, June 2012, American Chemical Society (ACS)

    Dmitrii Makarov

  22. Charge‐Site‐Dependent Dissociation of Hydrogen‐Rich Radical Peptide Cations upon Vacuum UV Photoexcitation

    Article • Chemistry - A European Journal, March 2012, Wiley

    Dmitrii Makarov

  23. Entropic and Electrostatic Effects on the Folding Free Energy of a Surface-Attached Biomolecule: An Experimental and Theoretical Study

    Article • Journal of the American Chemical Society, January 2012, American Chemical Society (ACS)

    Dmitrii Makarov, Professor Francesco Ricci

  24. Individual Proteins Under Mechanical Stress: Lessons from Theory and Computer Simulations

    Article • January 2012, Springer Science + Business Media

    Dmitrii Makarov

  25. Milestoning with transition memory

    Article • The Journal of Chemical Physics, December 2011, American Institute of Physics

    Dmitrii Makarov

  26. The effect of a mechanical force on quantum reaction rate: Quantum Bell formula

    Article • The Journal of Chemical Physics, November 2011, American Institute of Physics

    Dmitrii Makarov

  27. Chemical reactions modulated by mechanical stress: Extended Bell theory

    Article • The Journal of Chemical Physics, October 2011, American Institute of Physics

    Dmitrii Makarov

  28. Molecular Weight Effect on the formation of β Phase Poly(9,9′-dioctylfluorene) in Dilute Solutions

    Article • The Journal of Physical Chemistry B, October 2011, American Chemical Society (ACS)

    Dmitrii Makarov

  29. Rigorous coarse-graining for the dynamics of linear systems with applications to relaxation dynamics in proteins

    Article • The Journal of Chemical Physics, August 2011, American Institute of Physics

    Dmitrii Makarov

  30. 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

    Article • The Journal of Chemical Physics, February 2011, American Institute of Physics

    Dmitrii Makarov

  31. Universality in the Timescales of Internal Loop Formation in Unfolded Proteins and Single-Stranded Oligonucleotides

    Article • Biophysical Journal, December 2010, Elsevier

    Dmitrii Makarov

  32. Communication: κ-dynamics—An exact method for accelerating rare event classical molecular dynamics

    Article • The Journal of Chemical Physics, November 2010, American Institute of Physics

    Dmitrii Makarov

  33. A Mechanistic Study of Electron Transfer from the Distal Termini of Electrode-Bound, Single-Stranded DNAs

    Article • Journal of the American Chemical Society, October 2010, American Chemical Society (ACS)

    Dmitrii Makarov

  34. The resistance curve for subcritical cracks near the threshold

    Article • International Journal of Fracture, August 2010, Springer Science + Business Media

    Dmitrii Makarov

  35. A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements

    Article • The Journal of Chemical Physics, July 2010, American Institute of Physics

    Dmitrii Makarov

  36. End-to-Surface Reaction Dynamics of a Single Surface-Attached DNA or Polypeptide

    Article • The Journal of Physical Chemistry B, February 2010, American Chemical Society (ACS)

    Dmitrii Makarov

  37. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes

    Article • The Journal of Chemical Physics, January 2010, American Institute of Physics

    Dmitrii Makarov

  38. Denoising Single-Molecule FRET Trajectories with Wavelets and Bayesian Inference

    Article • Biophysical Journal, January 2010, Elsevier

    Dmitrii Makarov

  39. De-Noising Single Molecule FRET Trajectories using Wavelent and Bayesian Techniques

    Article • Biophysical Journal, January 2010, Elsevier

    Dmitrii Makarov

  40. The Rate of Intramolecular Loop Formation in DNA and Polypeptides: The Absence of the Diffusion-Controlled Limit and Fractional Power-Law Viscosity Dependence

    Article • The Journal of Physical Chemistry B, September 2009, American Chemical Society (ACS)

    Dmitrii Makarov

  41. Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency

    Article • The Journal of Chemical Physics, August 2009, American Institute of Physics

    Dmitrii Makarov

  42. Pitfalls of choosing an order parameter for rare event calculations

    Article • The Journal of Chemical Physics, August 2009, American Institute of Physics

    Dmitrii Makarov

  43. The Length and Viscosity Dependence of End-to-End Collision Rates in Single-Stranded DNA

    Article • Biophysical Journal, July 2009, Elsevier

    Dmitrii Makarov

  44. ChemInform Abstract: Computer Simulations and Theory of Protein Translocation

    Article • ChemInform, May 2009, Wiley

    Dmitrii Makarov

  45. Comment on “Asymptotic Strength Limit of Hydrogen-Bond Assemblies in Proteins at Vanishing Pulling Rates”

    Article • Physical Review Letters, March 2009, American Physical Society (APS)

    Dmitrii Makarov

  46. A Kinetic Model for the Enzymatic Action of Cellulase

    Article • The Journal of Physical Chemistry B, March 2009, American Chemical Society (ACS)

    Dmitrii Makarov

  47. A Theoretical Model for the Mechanical Unfolding of Repeat Proteins

    Article • Biophysical Journal, March 2009, Elsevier

    Dmitrii Makarov

  48. Computer Simulations and Theory of Protein Translocation

    Article • Accounts of Chemical Research, December 2008, American Chemical Society (ACS)

    Dmitrii Makarov

  49. Translocation of a knotted polypeptide through a pore

    Article • The Journal of Chemical Physics, September 2008, American Institute of Physics

    Dmitrii Makarov

  50. Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors

    Article • Physical Biology, June 2008, Institute of Physics Publishing

    Dmitrii Makarov

  51. The rate constant of polymer reversal inside a pore

    Article • The Journal of Chemical Physics, March 2008, American Institute of Physics

    Dmitrii Makarov

  52. Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study

    Article • The Journal of Chemical Physics, March 2008, American Institute of Physics

    Dmitrii Makarov

  53. Simulations of the untying of molecular friction knots between individual polymer strands

    Article • The Journal of Chemical Physics, March 2008, American Institute of Physics

    Dmitrii Makarov

  54. Unraveling Individual Molecules by Mechanical Forces: Theory Meets Experiment

    Article • Biophysical Journal, June 2007, Elsevier

    Dmitrii Makarov

  55. Influence of local and residual structures on the scaling behavior and dimensions of unfolded proteins

    Article • Biopolymers, April 2007, Wiley

    Dmitrii Makarov

  56. Single-Molecule Electrophoresis of β-Hairpin Peptides by Electrical Recordings and Langevin Dynamics Simulations

    Article • The Journal of Physical Chemistry B, March 2007, American Chemical Society (ACS)

    Dmitrii Makarov

  57. Computer simulations of protein translocation

    Article • physica status solidi (b), July 2006, Wiley

    Dmitrii Makarov

  58. Computer simulations of protein translocation

    Article • physica status solidi (b), July 2006, Wiley

    Dmitrii Makarov

  59. Mechanical Unfolding of Segment-Swapped Protein G Dimer:  Results from Replica Exchange Molecular Dynamics Simulations

    Article • The Journal of Physical Chemistry B, July 2006, American Chemical Society (ACS)

    Dmitrii Makarov

  60. On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data

    Article • The Journal of Chemical Physics, February 2006, American Institute of Physics

    Dmitrii Makarov

  61. Evidence for Non-Two-State Kinetics in the Nucleocapsid Protein Chaperoned Opening of DNA Hairpins

    Article • The Journal of Physical Chemistry B, January 2006, American Chemical Society (ACS)

    Dmitrii Makarov

  62. Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore

    Article • The Journal of Chemical Physics, September 2005, American Institute of Physics

    Dmitrii Makarov

  63. Site-specific Dimensions Across a Highly Denatured Protein; A Single Molecule Study

    Article • Journal of Molecular Biology, September 2005, Elsevier

    Dmitrii Makarov

  64. Topography of the free-energy landscape probed via mechanical unfolding of proteins

    Article • The Journal of Chemical Physics, June 2005, American Institute of Physics

    Dmitrii Makarov

  65. Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single-molecule pulling experiments

    Article • Physical Review E, February 2005, American Physical Society (APS)

    Dmitrii Makarov, Professor Kilho Eom

  66. Translocation of a β-hairpin-forming peptide through a cylindrical tunnel

    Article • The Journal of Chemical Physics, November 2004, American Institute of Physics

    Dmitrii Makarov

  67. Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding reaction coordinates by changing the pulling geometry

    Article • The Journal of Chemical Physics, September 2004, American Institute of Physics

    Dmitrii Makarov

  68. Ubiquitin-like Protein Domains Show High Resistance to Mechanical Unfolding Similar to That of the I27 Domain in Titin:  Evidence from Simulations

    Article • The Journal of Physical Chemistry B, December 2003, American Chemical Society (ACS)

    Dmitrii Makarov

  69. Theoretical studies of the mechanical unfolding of the muscle protein titin: Bridging the time-scale gap between simulation and experiment

    Article • The Journal of Chemical Physics, November 2003, American Institute of Physics

    Dmitrii Makarov

  70. Relationship between the Mechanical Properties and Topology of Cross-Linked Polymer Molecules:  Parallel Strands Maximize the Strength of Model Polymers and Protein Domains

    Article • The Journal of Physical Chemistry B, August 2003, American Chemical Society (ACS)

    Dmitrii Makarov, Professor Kilho Eom

  71. Nanosecond Dynamics of Single Polypeptide Molecules Revealed by Photoemission Statistics of Fluorescence Resonance Energy Transfer:  A Theoretical Study

    Article • The Journal of Physical Chemistry B, May 2003, American Chemical Society (ACS)

    Dmitrii Makarov

  72. Molecular nanosprings in spider capture-silk threads

    Article • Nature Materials, March 2003, Springer Science + Business Media

    Dmitrii Makarov

  73. Response to “Comment on ‘On the interpretation of force-extension curves of single protein molecules’ ” [J. Chem. Phys. 118, 2964 (2003)]

    Article • The Journal of Chemical Physics, February 2003, American Institute of Physics

    Dmitrii Makarov

  74. Rate of intramolecular contact formation in peptides: The loop length dependence

    Article • The Journal of Chemical Physics, September 2002, American Institute of Physics

    Dmitrii Makarov

  75. Configurational entropy and mechanical properties of cross-linked polymer chains: Implications for protein and RNA folding

    Article • July 2002, American Physical Society (APS)

    Dmitrii Makarov

  76. On the interpretation of force extension curves of single protein molecules

    Article • The Journal of Chemical Physics, May 2002, American Institute of Physics

    Dmitrii Makarov

  77. Observation of single molecule transport at surfaces via scanning microscopies: Monte Carlo wave function study of a model problem

    Article • April 2002, American Physical Society (APS)

    Dmitrii Makarov

  78. A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results

    Article • The Journal of Chemical Physics, March 2002, American Institute of Physics

    Dmitrii Makarov

  79. 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

    Article • The Journal of Chemical Physics, October 2001, American Institute of Physics

    Dmitrii Makarov

  80. Kinetic Monte Carlo simulation of titin unfolding

    Article • The Journal of Chemical Physics, June 2001, American Institute of Physics

    Dmitrii Makarov

  81. Using Genetic Programming To Solve the Schrödinger Equation

    Article • The Journal of Physical Chemistry A, August 2000, American Chemical Society (ACS)

    Dmitrii Makarov

  82. Quantum dynamics with dissipation: A treatment of dephasing in the stochastic Schrödinger equation

    Article • The Journal of Chemical Physics, December 1999, American Institute of Physics

    Dmitrii Makarov

  83. Stochastic Schrödinger equation. II. A study of the coherence seen in pump-probe experiments that use a strong pump laser

    Article • The Journal of Chemical Physics, December 1999, American Institute of Physics

    Dmitrii Makarov

  84. RAW quantum transition state theory

    Article • June 1998, World Scientific Pub Co Pte Lt

    Dmitrii Makarov

  85. 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

    Article • The Journal of Chemical Physics, May 1998, American Institute of Physics

    Dmitrii Makarov

  86. van der Waals Energies in Density Functional Theory

    Article • Physical Review Letters, May 1998, American Physical Society (APS)

    Dmitrii Makarov

  87. Fitting potential-energy surfaces: A search in the function space by directed genetic programming

    Article • The Journal of Chemical Physics, January 1998, American Institute of Physics

    Dmitrii Makarov

  88. The reaction rate constant in a system with localized trajectories in the transition region: Classical and quantum dynamics

    Article • The Journal of Chemical Physics, November 1997, American Institute of Physics

    Dmitrii Makarov

  89. Control of dissipative tunneling dynamics by continuous wave electromagnetic fields: Localization and large-amplitude coherent motion

    Article • December 1995, American Physical Society (APS)

    Dmitrii Makarov

  90. On the transition from electronically nonadiabatic to solvent-controlled electron transfer

    Article • Chemical Physics Letters, November 1995, Elsevier

    Dmitrii Makarov

  91. Non-Poisson statistics of reactive events and nonexponential kinetics

    Article • September 1995, American Physical Society (APS)

    Dmitrii Makarov

  92. Stochastic resonance and nonlinear response in double-quantum-well structures

    Article • July 1995, American Physical Society (APS)

    Dmitrii Makarov

  93. Quantum transition-state theory below the crossover temperature

    Article • July 1995, American Physical Society (APS)

    Dmitrii Makarov

  94. Tensor propagator for iterative quantum time evolution of reduced density matrices. I. Theory

    Article • The Journal of Chemical Physics, March 1995, American Institute of Physics

    Dmitrii Makarov

  95. Tensor propagator for iterative quantum time evolution of reduced density matrices. II. Numerical methodology

    Article • The Journal of Chemical Physics, March 1995, American Institute of Physics

    Dmitrii Makarov

  96. Path integrals for dissipative systems by tensor multiplication. Condensed phase quantum dynamics for arbitrarily long time

    Article • Chemical Physics Letters, April 1994, Elsevier

    Dmitrii Makarov

  97. Advances in Chemical Physics

    Article • January 1994

    Dmitrii Makarov

  98. Quantum versus classical control of tunneling

    Article • December 1993, American Physical Society (APS)

    Dmitrii Makarov

  99. Tunneling dynamics in dissipative curve-crossing problems

    Article • Physical Review A, November 1993, American Physical Society (APS)

    Dmitrii Makarov