All Stories

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Computational and Theoretical Insights into Protein and Peptide Translocation

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

    Dmitrii Makarov

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

    Article • Protein Science, September 2013, Wiley

    Dmitrii Makarov

  13. 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

  14. 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

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

    Article • Biophysical Journal, June 2013, Elsevier

    Dmitrii Makarov

  16. 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

  17. 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

  18. 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

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

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

    Dmitrii Makarov

  20. 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

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

    Article • January 2012, Springer Science + Business Media

    Dmitrii Makarov

  22. Milestoning with transition memory

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

    Dmitrii Makarov

  23. 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

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

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

    Dmitrii Makarov

  25. 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

  26. 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

  27. 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

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

    Article • Biophysical Journal, December 2010, Elsevier

    Dmitrii Makarov

  29. 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

  30. 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

  31. The resistance curve for subcritical cracks near the threshold

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

    Dmitrii Makarov

  32. 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

  33. 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

  34. 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

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

    Article • Biophysical Journal, January 2010, Elsevier

    Dmitrii Makarov

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

    Article • Biophysical Journal, January 2010, Elsevier

    Dmitrii Makarov

  37. 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

  38. 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

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

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

    Dmitrii Makarov

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

    Article • Biophysical Journal, July 2009, Elsevier

    Dmitrii Makarov

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

    Article • ChemInform, May 2009, Wiley

    Dmitrii Makarov

  42. 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

  43. A Kinetic Model for the Enzymatic Action of Cellulase

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

    Dmitrii Makarov

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

    Article • Biophysical Journal, March 2009, Elsevier

    Dmitrii Makarov

  45. Computer Simulations and Theory of Protein Translocation

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

    Dmitrii Makarov

  46. Translocation of a knotted polypeptide through a pore

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

    Dmitrii Makarov

  47. 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

  48. The rate constant of polymer reversal inside a pore

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

    Dmitrii Makarov

  49. 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

  50. 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

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

    Article • Biophysical Journal, June 2007, Elsevier

    Dmitrii Makarov

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

    Article • Biopolymers, April 2007, Wiley

    Dmitrii Makarov

  53. 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

  54. Computer simulations of protein translocation

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

    Dmitrii Makarov

  55. Computer simulations of protein translocation

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

    Dmitrii Makarov

  56. 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

  57. 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

  58. 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

  59. 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

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

    Article • Journal of Molecular Biology, September 2005, Elsevier

    Dmitrii Makarov

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. Molecular nanosprings in spider capture-silk threads

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

    Dmitrii Makarov

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. Kinetic Monte Carlo simulation of titin unfolding

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

    Dmitrii Makarov

  78. Using Genetic Programming To Solve the Schrödinger Equation

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

    Dmitrii Makarov

  79. 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

  80. 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

  81. RAW quantum transition state theory

    Article • June 1998, World Scientific Pub Co Pte Lt

    Dmitrii Makarov

  82. 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

  83. van der Waals Energies in Density Functional Theory

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

    Dmitrii Makarov

  84. 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

  85. 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

  86. 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

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

    Article • Chemical Physics Letters, November 1995, Elsevier

    Dmitrii Makarov

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

    Article • September 1995, American Physical Society (APS)

    Dmitrii Makarov

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

    Article • July 1995, American Physical Society (APS)

    Dmitrii Makarov

  90. Quantum transition-state theory below the crossover temperature

    Article • July 1995, American Physical Society (APS)

    Dmitrii Makarov

  91. 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

  92. 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

  93. 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

  94. Advances in Chemical Physics

    Article • January 1994

    Dmitrii Makarov

  95. Quantum versus classical control of tunneling

    Article • December 1993, American Physical Society (APS)

    Dmitrii Makarov

  96. Tunneling dynamics in dissipative curve-crossing problems

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

    Dmitrii Makarov